Hiring your real estate agent:
The easiest way to search property in Japan, is to hire an English speaking real estate agent. Let them do all of the hassle work for you, including negotiations. Before you start to look for an agent, educate yourself on the following issues:
1) MLS (Multiple Listing Services) is available
Most of the property information about available homes for rent and for sale, are available on the MLS database. Licensed real estate agents share this information. So even if you contact a number of agencies, the information will not be much different. As long as you can find a good agent, you won't need to solicit the help of multiple agencies.
2) Commission in Japan
You will pay commission for your agent. That is standard practice in Japan. The benefit of this system is that it becomes very clear who the agent represents.
3) Standard commission for rent
The fee is equivalent to one month's rent, plus consumption tax (currently 5%). You pay this fee when you sign the rental agreement with the landlord. If you don't obtain a result, you absolutely have no obligation to pay them anything.
4) Standard commission for purchase
The fee is equivalent to 3% of the purchase price, plus consumption tax (currently 5%). You pay 50% of this fee when you sign the purchase agreement with the seller. You pay the 50% balance upon closing the deal (title transferred). If you don't obtain a result, you absolutely have no obligation to pay them anything.
5) Direct contact with developers
Some developers and apartment owners offer in-house agent services in English. In most cases, they will not charge a fee for this service, so you can contact them directly without hiring an agent. The only issue you need to be aware of, is that the agent represents the owner. So prepare to negotiate effectively on your own behalf and make sure all conditions are acceptable.