The central bank, which is working to regain public trust after its governor's private investment scandal, said it has normally paid travel expenses, such as airfare, in advance based on the cost of regular tickets.
But many officials bought discount tickets and kept the difference because the bank did not ask for receipts, the central bank said in an internal investigation report, released after numerous media leaks.
The bank said it has reprimanded and issued warnings to 41 officials, along with an unspecified number of officials who were talked to by supervisors.
"The bank will order the affected officials to return excessive payments," the Bank of Japan report said.
The scandal came as the central bank tries to regain public trust, following a highly public scandal involving Governor Toshihiko Fukui.
The central banker admitted profiting through investment in a fund managed by high-profile former bureaucrat Yoshiaki Murakami, who was later arrested on insider trading charges.