The crash happened on the A90 Aberdeen to Peterhead road at Auchiries, Longhaven, near Peterhead.
The 46-year-old officer was in a critical condition while the 58-year-old male car driver was stable.
Police Scotland said two police dogs in the van survived. One was uninjured, the other was being assessed.
The accident happened at about 23:50 on Tuesday.
Both drivers were freed from their vehicles before being taken to Aberdeen Royal Infirmary for treatment.
Relatives of the police officer have been informed.
Insp Jon Barron said: "Our inquiries into the circumstances of this crash are obviously still at an early stage.
"I would be very keen to speak with anyone who may have seen either vehicle shortly beforehand, or anyone who witnessed the collision and who hasn't yet been spoken to by police. Please contact us on 101."
The A90 was closed for several hours while collision investigators studied the scene and examined both vehicles.
The road has since re-opened.
A police dog handler has been left critically injured after his van was involved in a crash with a car on the A90 in Aberdeenshire.