A statement from Maritimes Forces Pacific said that at the time of the crash, the HMCS Winnipeg was tied up alongside the force's base jetty.
BC Ambulance Service said its crews took six people to Victoria General Hospital with what were classified as minor injuries.
Larry Edwards was nearby at the time of the collision and watched the large trawler ram the much smaller warship.
"When it hit, there was a wall of water that came up over the bow of the Winnipeg that was higher than the bow. It washed right over on the other side," he said.
"I saw the Winnipeg move back on the dock a good 20, 30 feet, it really shifted it."
The amount of damage to the ships was unclear, but the warship and the trawler, owned by the American Seafoods Co. based in Seattle, remained joined at the bows for much of the day.
American Seafoods released a brief statement confirming the collision involving it's fishing vessel, American Dynasty.
"The cause of the collision is currently under investigation. American Seafoods and the vessel crew are co-operating fully with Canadian and U.S. authorities.
The Winnipeg has been under a refit as part of an estimated $4.5 billion dollar upgrade for Canadian naval ships.