There were plans to use a remote operated vehicle for a closer look at the Ann Harvey to prepare for temporary repairs, said spokeswoman Jan Woodford.
Capt. Jim Chmiel said the light icebreaker was anchored in a sheltered harbour off Newfoundland's southwest coast near Burgeo after being towed early Thursday by the coast guard ship Louis S. St-Laurent. He said pumps were working to remove water from the propulsion motor room and the after-sewage compartment that had flooded.
Two cadets were taken off the icebreaker late Wednesday, but the remaining 26 crew members stayed on board. There were no injuries reported.
Chmiel said it's not yet clear why the ship struck the shoal, but an investigation will begin once repairs are done and the ship is towed back to St. John's.
The Ann Harvey is a light icebreaker built in Halifax in 1987. The diesel-electric ship can carry 47 people. Its other duties include tending buoys, search and rescue missions, and fisheries enforcement.
The ship was moving navigation buoys when it hit bottom but it was not considered in danger of sinking.
Its removal from service during one of the worst ice seasons in decades is not expected to affect passenger ferries "given existing ice conditions," Woodford said.
"There may be some delays with our harbour breakout schedule," she said of how icebreakers are used to help clear ports where commercial services aren't available.
Otherwise, the coast guard will move light icebreakers throughout the region as required, Woodford said.
Conditions have improved in the last couple of weeks since a Marine Atlantic ferry was stuck for more than two days in thick pack ice off Cape Breton. The MV Blue Puttees was about 35 kilometres from port in North Sydney with 40 passengers and commercial freight onboard.
Marine Atlantic spokesman Darrell Mercer said it's never a good time for the coast guard to lose even a lighter icebreaker.
"It just adds extra challenges to their decision-making process of where they allocate resources at any particular time," he said in an interview. "There's a lot of ice that's still in the Cabot Strait area. While wind conditions over the past number of days have been favourable, the forecast of course can change at a moment's notice.
"We'll continue to watch those and keep our fingers crossed that maybe Mother Nature's finally going to give us a break."
Randy Edmunds, the provincial Liberal critic for Labrador affairs, has repeatedly raised concerns about inadequate coast guard services that leave passengers stranded and store shelves empty.
"It's unfortunate to lose an icebreaker in a situation where we were pressed for icebreakers to start with," he said in an interview.
"We've come to depend on the ferries for passenger service as well as freight delivery. And once those vessels can't get there, everyone is compromised."
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