The news is a hefty blow to Button's hopes of victory and follows a series of technical failings which have bedevilled his McLaren team in the last month.
Button retired from second place in the Italian Grand Prix and team-mate Lewis Hamilton was forced out of the Singapore GP while leading the race when his gearbox failed.
According to Autosport, Button's gearbox has now also been changed after analysis determined that it would suffer the same race-ending shutdown as Hamilton's two weeks ago.
"Jenson's gearbox had the same problem as Lewis's gearbox during the Singapore Grand Prix, and subsequent investigation has revealed a terminal failure," said Technical Director Paddy Lowe.
"Therefore both cars must start the Japanese Grand Prix with new gearboxes, which means that Jenson will receive a five-place penalty."
Hamilton, however, will not receive a penalty having retired from the Singapore race.