ANA said the flight had been diverted "due to fog". It had been scheduled to land at Frankfurt at 05:25.
Meteorological data for Frankfurt at the time indicated fog, overcast skies and low visibility.
Similar conditions prevailed at other nearby hubs including Paris Charles de Gaulle and Munich.
The aircraft subsequently departed for Frankfurt ahead of operating the return NH204 service back to Tokyo Haneda. ANA has five 787s in service, all powered by Rolls-Royce Trent 1000 engines.