It is understood the bike was not being pursued when the incident happened.
The road was sealed off for several hours while investigations got under way.
An incident response unit, as well as a police van and two police cars, were at the scene while officers pieced together the lead-up to the incident.
A police spokeswoman confirmed incident will be referred to PIRC.
She said: “At around 2.50am on Saturday, April 22, police received a report of a road traffic collision involving a police van and a motorcycle on Granitehill Road, Aberdeen.
“The male motorcyclist, aged 35, has been taken to hospital. No one else sustained any injuries in the incident and inquiries are ongoing to establish the circumstances of the crash.”
Biker in hospital following collision with police van