MOFA's 34mm Head
35x45mm with the head at 34mm, plus or minus 2mm.
Japan's Ministry of Foreign Affairs publishes the head height as 34mm ±2mm, which gives a practical range of 32mm to 36mm from chin to crown within the 35x45mm frame.
This matches the standard ICAO geometry, so a Japanese passport photo is the same shape as a Schengen or Australian one. What differs is how the print itself is judged.