According to the Ministry of Land, Infrastructure, Transport, and Tourism (MLIT), you do not need permission to fly a drone as long as you intend to operate your drone in non-prohibited airspace and follow all operational limitations.
If you intend to operate your drone in the following airspaces, you are required to obtain permission from the MLIT.
You are required to follow the operational conditions listed below unless approved by the MLIT.
While many high-end drone makers have the no-fly zones and restrictions in their flight computer’s software preloaded, it is still the responsibility of the pilot to be completely aware of the regulations and allowed airspace. There is a free map that shows you where you can fly courtesy drone maker DJI:
Just enter the place you’d like to go to in the field on the top of the page. Red means a no-fly zone unless you have special permission. Please be advised that you may face the maximum ¥500,000 penalty if you fail to meet these restrictions, and check the official MLIT site for the most up to date information.