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Accounting & Management  ·  Minato International Accounting Office

Many companies maintain accounts primarily to satisfy tax and statutory obligations. That is a reasonable starting point — but it leaves most of the value of bookkeeping on the table. Well-designed accounting records answer the questions that business owners actually ask.

Here are four principles we consistently apply when helping foreign-affiliated companies set up their books in Japan.


1. Record transactions when they happen, not when cash moves

Cash-basis bookkeeping is simple, but it distorts the picture. A profitable month can look like a loss if several large invoices happen to be outstanding. A weak month can look healthy if an old receivable finally gets paid.

Accrual-basis accounting ties revenue and expenses to the period in which they are earned or incurred. The result is a P&L that reflects what actually happened in the business — not an artefact of payment timing. For any company that carries receivables, payables, or inventory, this distinction is fundamental.

2. Know your balance sheet one line deeper

A balance sheet that shows “accounts receivable: ¥12,000,000” is a starting point, not an answer. The useful question is: which customers owe how much, and for how long?

Maintaining balances at the sub-account level — by customer, by vendor, by individual asset — makes it possible to spot concentration risk, chase overdue invoices, and respond to auditor queries without reconstructing data from scratch. The same logic applies to fixed assets, prepaid expenses, and accrued liabilities. Aggregate figures are fine for reporting; granular records are what allow you to act.

3. Allocate every transaction to a cost center

Consolidated P&L is a useful health check. But it rarely tells you where a problem originates or where an opportunity lies. Department-level accounting — allocating revenue and costs to divisions, product lines, projects or even each employees at the point of entry — makes it possible to compare performance across the business and hold each unit accountable for its results.

This matters most when the business has more than one product line, service category, or location. Without department-level allocation, a healthy division can mask a struggling one — and by the time the problem becomes visible in the overall P&L, it is already late to act. Assigning costs and revenue to the right unit from the start means you always know which part of the business is pulling its weight, and which needs attention.
The same logic applies at a finer level. When transactions are allocated to individual team members or staff, the books can reflect not just what the business earned, but who generated it. And allocation works in both directions: expenses — travel, materials, subcontractors, or any cost tied to a specific person’s work — can be assigned to the same staff member or team. Salary costs are no different. When payroll is allocated to the people or projects it relates to, the true cost of each staff member’s contribution becomes visible. The result is a genuine picture of margin delivered, not just revenue generated — which, for a service business where people are the primary cost, is the number that actually matters.

4. Make the numbers accessible to the people who need them

Accounting records that live on a single accountant’s desktop — or arrive as a PDF attachment once a month — are not management information. They are historical documents.

When authorised users can access current figures from anywhere, the books become a live resource. The CFO travelling overseas can check cash position before a decision. The operations manager can review departmental costs without waiting for a report. The external auditor can work from the same data without requesting extracts. Accessibility is not a convenience feature; it changes how the information gets used.


At Minato International Accounting Office, we apply these principles through InsightBooks, our in-house accounting platform developed specifically for foreign-affiliated companies in Japan. If you would like to discuss how your current bookkeeping setup could better support management decision-making, we are glad to help.

Contact Minato International Accounting Office →

If you are running a business in Japan as a foreign national or managing a foreign-affiliated company, this is one of the first questions you will ask. The short answer is: it depends. But for most businesses, the honest answer is — yes, you probably do.

Here is why.

Japan’s Tax System Is Complex — Especially Consumption Tax, Even for Japanese People

Japan has one of the most detailed tax systems in the world. Corporate tax, consumption tax, withholding tax, fixed asset tax, and payroll-related obligations all run on different schedules and follow different rules. Miss a deadline or misclassify an item, and the penalties can be significant (10% – 15%).

For a foreign business owner who is still navigating the language, the culture, and the market, adding tax compliance to the list is a serious burden.

What a Japanese Accountant Actually Does for You

A good accountant does far more than file your tax return once a year. They keep your books accurate on a monthly basis, flag issues before they become problems, advise you on tax-saving opportunities, and represent you in the event of a tax audit.

More importantly, they give you numbers you can trust — so you can focus on running your business instead of worrying about whether your records are correct.

When You Might Be Able to Manage Yourself

There are situations where self-management is feasible. If you are a sole proprietor with straightforward income and minimal expenses, and you are comfortable reading Japanese tax guidelines, you may be able to handle basic bookkeeping and tax filing on your own — at least in the early stages.

Cloud-based accounting software such as freee or MoneyForward has made this more accessible than it used to be. However, even these platforms require a solid understanding of Japanese accounting rules to use correctly.

The Hidden Cost of Getting It Wrong

Many foreign business owners try to manage alone at first, only to bring in an accountant later to clean up months — or years — of incorrect records. The cost of fixing mistakes is almost always higher than the cost of doing it right from the beginning.

There is also the question of opportunity cost. Every hour you spend on bookkeeping is an hour not spent on your customers, your product, or your growth.

What to Look for in a Japanese Accountant

Not all accounting firms are equipped to serve foreign-affiliated businesses. When choosing a firm, look for the following:

  • English-language communication capability
  • Experience with international taxation and cross-border transactions
  • Familiarity with the reporting requirements of foreign parent companies
  • A proactive approach — not just compliance, but genuine business advice

The Bottom Line

Japan rewards businesses that stay compliant, keep clean records, and plan ahead. A qualified Japanese accountant is not just a cost — they are an investment in the stability and growth of your business.

If you are serious about building something in Japan, get the right support from the start.


Minato International Accounting Office specializes in serving foreign-affiliated companies in Japan. We provide English-language bookkeeping, tax filing, and business advisory services — so you can focus on what you do best.

There are lots of businesses that receive orders from customers overseas and buy goods in Japan for margins. We also have several clients doing the business too. Their margins are relatively low in many cases that is mostly in the range between 1% to 10%. Some businesses only charges 300 yen per item. Still they are surviving and sometime very profitable. Why?

It’s because their source of profit is not only the fees on their price tag but also a hidden source of profit that is not very visible from eyes of customers overseas. They count on Japanese Consumption Tax refund that is 10% of the price itself.

However, there is a potential issue here. If they are buying goods just on behalf of customers, they may be regarded merely as an agent and will not get the tax refund.

The rule of thumb is that the consumption tax is refundable only to real buyers. If they are buying goods in Japan on behalf of somebody like an agent, that somebody behind you should be the one to receive refund. There is a risk that the tax office say no to the refund claim for those purchasing things on behalf because the tax office can think that the real buyer is not the one who makes purchases in Japan and claims refund but his customers overseas.

The line between an agent and a dealer is a bit vague.

What you should do to avoid the situation?

You want to make it clear that you are buying and selling like a dealer. Please take a receipt under your name (not your customers’ name). On your invoice to customer, please make sure that you are selling goods that are bought for your customers. You are not just charging your fees of certain percentages. If you are displaying to your customers that your fee is certain percentage, what you are doing is agent. Your need to change your substance of your business model from being an agent to a dealer.

Also when you ship it, you may need to get an export permission (輸出許可証). Take it under your name.

I would like to make it clear that it is perfectly legal to receive orders from customers first and then buy and sell. Taking orders from customers for specific goods does not necessarily means that you are buying things as an agent. Civil Law article #561 allows to have an agreement to sell which is not under your possession yet.

Who bare the risk of hidden problem?

One of the criteria when it comes to a tax audit is whether you will take responsibility and risk of the goods delivery. For example, you had a car accident and damaged your goods, would you be paid or you would not? If the answer is yes, your customer is taking the risk and you do not. The legal implication may be that the ownership of the goods are already transferred to the owner even before physical delivery.

Who pay insurance?

Another factor to determine whether ownership is transferred to your buyer before the delivery is who pays for insurance. If insurance is paid by your customer, it suggests more that the buyer already owns the goods.

If you have only one customer and make purcahses exclusively for him, you are at risk. You may be seen as an agent of the customer.

Free consultation

If you have any concerns or you are already in trouble with the tax audit, we are happy to provide a consultation for free. Please contact through our contact form.

Consumption Tax Filer banner

 

Individuals or small capital companies (with paid-in capitals under 10 million yen) can elect the tax filer status or non-filer status of Consumption Tax during the first 2 years from the inception of the business or its incorporation. The default status is the non-filer, so unless you elect otherwise, you will automatically be a non-filer of Japanese Consumption tax.

 

If you expect sales in the first 2 years, your choice should be the non-filer status because you can pocket the consumption tax on sales (minus the consumption tax on expenses).

 

But there are a few situations where you will benefit from choosing the consumption tax filer status.

1) If your business requires a large amount of initial investment such as restaurants or accommodations, your choice should probably be the tax filer status.

2) If your sales are expected to come from overseas. You should definitely elect the consumption tax filer status. You will always get a consumption tax refund.

 

Here are the reasons why:

1) The consumption tax is payable between what you receive on sales and what you pay on expenses. If you are planning to start a restaurant and will heavily invest in kitchen equipment and interior decorations, whose investments will only be recovered after 3 years of business, you should apply for the consumption tax filer status and get a refund of 10% of the investment.

2) Consumption tax liability is the difference between what you receive and what you pay. You will not receive Japanese consumption tax on revenue from overseas, so if you do not receive any consumption tax from domestic sales and pay consumption tax on your domestic expenses for day-to-day operations, the balance will be negative. A negative balance means you will be refunded for it. Remember that the consumption tax is for consumers, not businesses.

 

Please note that it does not matter whether your sales are services (e.g. consultation) or things (e.g. export of Japanese Sake for example).

 

The downside is that once you elect to be a consumption tax filer, you will have to stay as one for at least the next 2 years. However, if you purchase a fixed asset such as machines or software that costs more than 1 million yen, it will be 3 years. So, you have to weigh which status is more beneficial in cash flow over the course of 2 or 3 years.

Gift tax is very expensive in Japan. You can see the tax rates as follows. It can even be prohibitive.

Net taxable gift after base deduction Under 2M JPY Under 3M JPY Under 4M JPY Under 6M JPY Under 10M JPY Under 15M JPY Under 30M JPY Over 30M JPY
Tax Rates 10% 15% 20% 30% 40% 45% 50% 55%
Deduction -0.1M -0.25M/td> -0.65M -1.25M -1.75M -2.5M 1.0M

Your parents may want to give their estate before they pass away and when you are still young to spend on something (e.g. children’s education, business investment, etc). But the gift tax is so expensive. What to do?

One solution is Early Inheritance (相続時精算課税).

You can choose to file your gift tax in future as Early Inheritance. The tax is free upto the first 25MM yen. Any gift after 25MM yen will be subject to 20% advance tax. If the total money you have received as an early inheritance is 50MM yen, the advance tax will be 5MM yen ((50M-25M) * 20%). Then, you will calculate your inheritance by the normal method and pay the difference if the actual tax is higher than the advance tax or you will receive a refund if the advance tax is higher.

  1. Ex-Works and Ex-Factory

 

When a company engages in business with a customer located overseas, it’s easy to assume that because the transaction is considered an export, it is exempt from taxation. It is also often presumed that consumption tax for any accompanying domestic expenses is eligible for refund.

 

You may already be familiar with the term tax-free export, but it’s important to be aware of the pitfalls.  

 

In some instances, even tax-free exports are not tax-exempt. A lot of businesses find navigating the specifics surrounding consumption tax to be challenging. Even tax accountants find it difficult – me included! If you get a call from the taxation office, don’t give up right away. It’s worth being persistent, as the final decision boils down to the facts.

 

There are various types of export transactions, the most well-known being Cost, Insurance, and Freight (CIF) and Free on Board (FOB).

 

Transactions that start with the letters C, D, and F are safe, but be careful with those that start with the letter E, such as Ex-Works and Ex-Factory.

 

According to Incoterms, under CIF, the seller is responsible for all costs, insurance and freight until the international vessel reaches the destination. Once the goods reach the destination, risk is transferred to the buyer as they bear all responsibility and liability thereafter. This transaction is considered an export.

http://ja.wikipedia.org/wiki/インコタームズ

 

The FOB rule states that the seller assumes payment of all costs until the goods reach the departing port and are loaded onto the vessel, at which point risk is transferred to the buyer, as they assume responsibility and liability thereafter. Because the cargo is loaded onto an international vessel (or airplane), this transaction is also considered an export.

 

Ex-Works and Ex-Factory are the terms that we need to watch out for. According to Incoterms, under Ex-Works and Ex-Factory, the transfer of risk occurs as soon as the goods are produced and packaged. The buyer is responsible for loading the goods for transport, and must pay all freight, insurance, and bear all other risks. In other words, in these cases a foreign buyer travels all the way to the factory in Japan just to pick up their goods.

 

When a customer travels all the way to a factory in Japan to collect goods, this becomes a domestic transaction. The consumption tax on these goods do not quality for exemption, and tax payment is due at the end of the term.

 

  1. A simple misprint on the export permit may have significant consequences.

 

An export permit must be obtained from the taxation office when exporting goods. Be sure to enter the correct information. For example, if you label an FOB transaction as Ex-works, the taxation office will take note, thus complicating the transaction.

 

A contract should clearly state the terms of sales, i.e., “CIF: risk is transferred at the destination,” to avoid confusion. However, if this information is omitted for some reason, you will have a challenging time proving the previously agreed upon terms of sale.  

 

For these reasons, it is very important to pay close attention to the details when obtaining an export permit.

 

  1. Precedents

Below is an example of a case brought before the National Tax Agency.

In this case, the taxation office’s decision to deny export tax exemption on a used vehicle shipped from Niigata to Russia was successfully overturned.

 

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