RCMP allege Cpl. Jason Prettie of Dauphin was working in Minnedosa when two weapons were stolen in 2009.
A spokeswoman says the rifle and shotgun were not police-issue and had been in RCMP custody.
The guns were found this year in a private residence connected to Prettie.
The officer has suspended with pay pending the outcome of his court case.
Prettie is also charged with obstructing justice and possession of a weapon obtained by crime.
He is to appear Tuesday in Dauphin provincial court.