The move follows calls for greater consistency from the officials during 2012, particularly in Moto2 and Moto3, where riders felt several incidents were treated either too leniently or with excessive harshness.
Up to 10 penalty points can be imposed, with sanctions applied at certain thresholds. Any rider reaching four penalty points starts the next race from the back of the grid, while seven points lead to a pitlane start and 10 points a race ban.
A statement from the Grand Prix Commission said: "It has been recognised that there is the need to address the problem of riders who are constantly being warned or penalised for endangering other riders or committing other serious offences like assaulting marshals or other officials.
"To address this issue a new system of penalty points was approved. Race Direction can sanction a rider with a number of penalty points between one and 10. This can be instead of or in addition to any other sanction."
The statement added: "Once the 10-point sanction has been imposed then points reset to zero. Points are not carried forward to the following season."
Moto2 champion Marc Marquez was involved in the season's highest-profile incidents and punishment. The 2013 Honda MotoGP signing was made to start from the back of the grid for the Valencia season finale after colliding with Simone Corsi in practice but went on to win the race.
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