The Observer newspaper reports the theft occurred last week in the Eastern Oregon city of La Grande.
The car was parked at the home of a trooper when someone smashed a window and took the firearm that had been in a mounted locked bracket.
State and La Grande police investigated the theft, and a team from the OSP Crime Lab in Pendleton assisted.
La Grande police Sgt. Gary Bell says it's extremely rare for a marked police vehicle to be the target of a break-in.