Police said Shepparton Crime Investigation Unit detectives activated their lights and sirens as they attempted to intercept a black Holden Statesman sedan on Albert St just before 10am.
Police allege the driver of the Holden failed to pull over and drove head-on into the unmarked police car on Victoria St before driving away.
The three officers onboard all received minor injuries while the police car received extensive front-end damage.
The Holden and driver were located in Law Street a short time later.
A 30-year-old Shepparton man was arrested at the scene.
A search of the stolen car located numerous edged weapons, police said.
While at the scene, police observed a stolen yellow Mini Coupe drive by about 10.20am.
With the assistance of Police Air Wing, police located the Mini in the driveway of a home on Colliver Rd.
Police claim the driver of the Mini reversed into a police car before driving away.
The unmarked police car received minor damage and the officers were uninjured.
The stolen Mini was quickly located by police in a multi-storey carpark on Stewart St.
A 17-year-old Yarrawonga boy, who police allege was the driver, was arrested on High St a short time later.
Both males remained in police custody late Thursday afternoon and were assisting police with their inquiries.