The trawler, American Dynasty, spent most of Tuesday with its bow crumpled into the side of the Canadian warship, but the vessels were finally separated late in the day.
The 90-metre trawler was being towed by tug boats when it broke away and hit Winnipeg, which was docked and undergoing a systems upgrade.
The Department of National Defence hasn't yet disclosed how badly Winnipeg or the jetty have been damaged.
They say an investigation continues and the Seattle-based company that owns the trawler is fully co-operating.
The six people hurt were not Canadian Forces personnel, but were civilian maintenance workers and crew from both ships. (CFAX)