Navy officials said the incident involving HMCS Winnipeg happened around 8 a.m. PT Tuesday at the jetty that CFB Esquimalt uses for mooring.
According to an eyewitness, at about 8:20 a.m. the American Dynasty trawler was leaving a big ship repair dock attached to the base.
The ship was being led out by two tugs when something went wrong.
Eyewitness Larry Edwards, who has an office that overlooks the scene, said it appeared the fishing vessel went forward when it should have gone backwards.
"They were backing it out in the harbour and as they were sort of swivelling the bow around, this thing sort of shot forward and slammed into the bow of the Canadian navy vessel," Edwards said.
"It hit hard. The wall of water that came up, it went over the bow of the navy vessel," he said.
On Tuesday, navy officials refused to comment on what might have occurred, saying only that the investigation is ongoing.
65 people were working on HMCS Winnipeg at the time of the crash.