Only minor injuries were reported from the fire, which began on Thursday around 10:20 p.m. PT, according to maritime forces public affairs.
The naval office said the fire was extinguished by sailors on board the ship, which is based in Esquimault, B.C.
HMCS Protecteur is currently about 340 nautical miles (630 km) northeast of Pearl Harbour, Hawaii.
The ship has limited power and is attempting to return to Peal Harbour, said Canadian navy officials. The U.S. navy has sent the destroyer USS Michael Murphy, to provide assistance to the Protecteur.
In the meantime, Protecteur personnel are conducting a full damage assessment.
In addition to the 279 crew members, there are 17 family members and two civilian contractors also on board.
The navy says having family members on board for the last part of a sail is a common practice with Royal Canadian Navy ships returning from extended operations and exercises.