Prior to now, such penalties were erased at the end of each season, with points and punishments accrued for a number of riding offences.
However, as part of a raft of new measures brought in by the FIM following a decision by the Grand Prix Commission, points will now stand for a year.
"From 2014 penalty points will remain on the record of the rider for 365 days after which they will be cancelled," the FIM said in a statement.
"This means that a rider will have a rolling tally of penalty points with new points being added as incurred and points being deducted on their anniversary."
Among other regulations to be introduced are a new set of guidelines to govern restarting races that are interrupted.
In all classes, any restarted races interrupted after less than five laps have been completed will be begin again, with Moto3 and Moto2 races limited to a maximum of two restarts.
More restarts can be sanctioned in MotoGP, according to the circumstances.