The remainder is owed to Japanese citizens and corporations. The remainder no doubt held by other central banks.
Meanwhile the prefectures and towns are not allowed to carry net debt. Granted various accounting tricks and lots of weirdness exists. Including a scheme where the federal government skips paying towns their transfer payments and instead tells them to borrow "on the federal government's behalf". This "favour debt" is then not reported as proper debt as the federal government has promised to pay the missing transfer payments, sometime, in the future.