The collision happened around 2:15 a.m. at Esplanade Avenue and State Street, according to the Riverside County Sheriff's Department.
The back end of the deputy's patrol vehicle was crushed by an impact with a light pole, while the front end of the civilian vehicle was also mangled.
The deputy, assigned to the sheriff's Hemet station, was responding to a call of service at the time of the collision, authorities said.
The critically injured deputy was rushed to a hospital, as was the driver of the other vehicle, who suffered moderate injuries.
Another deputy responding to the scene was also hurt while attempting to extricate the injured deputy. The second deputy was treated for a knee injury and released.
The intersection was closed for several hours as the California Highway Patrol conducted an investigation at the scene.
The cause of the crash was not immediately known.