The 64-year-old was elected just over a year ago on a campaign in which he vowed to get tough on crime.
But he caused uproar even before he was elected last year when stating that security forces accused of killing criminals "should be decorated and not have to go to court" to be held accountable for their actions.
It's not known how many members of the security forces have been pardoned in the measure that was signed by Bolsonaro on Monday night and published in the Official Journal on Tuesday.
The pardon covers those convicted of "crimes committed unintentionally" by members from all the different branches of the security forces, the presidency said.
It also pardons those convicted of crimes committed when off duty but done so with the intention of "eliminating a present risk to the self or third parties."
Those excluded from the order include people convicted of "terrible crimes" such as torture, terrorism or corruption, as well as serious disciplinary infractions.
Bolsonaro has come under fire over several policies since assuming power in January.
One proposed law from his Justice Minister Sergio Moro aimed at preventing police from being convicted over their actions during anti-crime operations was rejected by Congress.
Critics said it would give security forces impunity to commit unlawful killings.
Brazilian police, particularly in Rio de Janeiro state, have long been accused of heavy handed tactics when tackling crime in poor neighborhoods, known as favelas.
In the first quarter of the year, a record number of people -- 434 -- were killed by police in Rio during such interventions.
Bolsonaro also courted controversy in May by signing a decree relaxing rules on carrying guns.