A motorcyclist was taken to hospital after colliding with a police car in Baxter this morning.

Police have been told the motorcycle struck the rear passenger side of the unmarked police car on Frankston Flinders Road, near Peninsula Link overpass, about 1.45am.

The rider, carrying a stubby, tried to flee the scene before he collapsed off the bike a short distance away.

The 45-year-old was taken to hospital with minor injuries.

Two highway patrol members were not injured.

It is expected the Baxter man will be interviewed in relation to riding an unregistered bike.

Police will also investigate whether alcohol was a factor.