The incident happened at around 11am this morning in Kennoway, the two vehicles were involved in a crash on the A916, at Sandy Brae.
The female driver of the civilian car was taken to hospital by ambulance.
Images posted in Fife Jammer Locations showed damage to the police car.
Officers are now investigating the cause of the crash.
A Police Scotland spokesperson said: “Around 11.05am on Wednesday, 9 February, Road Policing Officers were called to a road crash involving a police car and another car on the A916 in Kennoway.
"A female driver was taken to hospital by ambulance to be checked over. The police officer did not require hospital treatment. Enquiries are ongoing into the cause of the crash.”