There are no legal restrictions on foreigners buying property in Japan. Regardless of visa status or even if one is a non-resident, anyone may acquire proprietary rights to Japanese real estate just like a Japanese national.
Similarly, the taxes regarding real estate such as Property registration & License tax, Property tax and City planning tax are levied on foreigners and Japanese nationals in the same way.
The main problem for foreigners to enter the residential real estate market is obtaining a home loan from a regular Japanese bank. Most Japanese banks will require residency of at least 3 years or permanent residency, and 3 years of Japanese tax returns, before they will consider someone for a home loan. On the other hand, if one is eligible for a home loan the interest rates on the mortgage can be astoundingly low – currently rates are often advertised as low as 0.7% for a 10 year fixed interest rate term.
For new condominiums it is typical to deal directly with the developer, but for other properties most buyers will use a real estate agent. In this case it is necessary to pay a brokerage fee (commission) of 3% of the purchase price plus 60,000 yen plus consumption tax (currently 8%) on the building portion, the land portion is not subject to the consumption tax. One can expect that registration fees and other taxes may add a further 3% or so to the purchase price. These fees are determined by the shihou shoshi, termed a legal scrivener, who is the type of lawyer responsible for property registration, and who is responsible for ensuring the property is free and clear of any liens or encumbrances.
The process of making an offer (a Letter of Intent) is fairly straightforward. In the offer it will be necessary to define the purchase price to be offered and the deposit (earnest money) which is usually around 10% of the purchase price. The odd thing about the Japanese system is that the terms of the Letter of Intent, particularly the price and the timing of the purchase, will have usually already been worked out verbally by the buyer’s real estate agent and the seller. Indeed, it is considered a loss of face for a Letter of Intent to be rejected on its face by the seller. This does not mean all deals go through.
Deals can still fall apart for various reasons (lack of financing for instance). But once the Letter of Intent is produced, and a corresponding letter from the seller confirming the acceptance of the terms (letter of conveyance), the basic contours of the deal are pretty well set.