A property in the Blaikes Quay area was sealed off at about 20:50 due to fears over the hazardous material.
The officers were taken to Aberdeen Royal Infirmary for further assessment. No-one else was affected.
A Police Scotland spokesman said: "There is no wider threat to the local community."
Scottish Ambulance Service and Scottish Fire and Rescue crews provided specialist decontamination assistance at the scene.
Five police officers have been taken to hospital after potentially coming into contact with asbestos during a routine search in Aberdeen harbour.