Button’s team-mate Lewis Hamilton, who last week revealed he will drive for Mercedes in 2013, retired from the last race in Singapore with a gearbox issue.
Drivers are required to use the same gearbox for five races, any unscheduled changes are punished by a grid penalty.
Although the gearbox on Hamilton’s car has also been changed, he does not serve a penalty as the problem caused him to retire in Singapore.
The penalty is a blow to Button’s hopes of recording back-to-back wins in Japan, and hauling back points in the title race.
The 2009 world champion currently sits sixth in the standings, 75 points adrift of Ferrari’s Fernando Alonso.
McLaren technical director Paddy Lowe told AUTOSPORT: "Jenson’s gearbox had the same problem as Lewis’ gearbox during the Singapore Grand Prix, and subsequent investigation has revealed a terminal failure.
"Therefore both cars must start the Japanese Grand Prix with new gearboxes, which means that Jenson will receive a five-place penalty."
Info: The National, Image: McLaren