Why does the IRS ask for an EIN number for a company in Japan, a foreign one?

If your income is from a foreign company -- they could not have issued any of the 1099s or W-2 and therefore no need for the EIN ( a foreign company with no substantial presence in the USA does not require an EIN ).

What are you trying to do ?

If you are acting as a consultant or a contract worker ( you a US citizen/resident ) and the work was done in the USA ( on line or otherwise), you report your income on schedule-C  ( sole ownership of a business , self-employed etc. ) and tell TurboTax that you do not have a 1099-MISC -- this will allow you to fill out the Schedule-C without the EIN.  Another way is to enter a dummy  EIN , like 38-123456 7 , print the return and snopake out the  EIN -- write NRA and send in by mail.