Canada's top general has reversed a decision by his head of the navy to mothball half of the country's coastal patrol vessels because they are too costly to upkeep.

Gen. Walter Natynczyk said Friday that he has scuttled Vice-Admiral Dean McFadden's order to tie up six out of 12 of the navy's maritime coastal defence vessels (MCDVs) because of funding shortfalls.

"I've ordered Admiral McFadden to rescind his instruction until we can have a look at the amount of resources the Canadian Forces can give him," he said.

Adm. McFadden wrote a letter to naval staff last month indicating that the fleet will pull half of its 12 defence patrols ships out of service permanently because they are too costly to upkeep.

"I have had to make difficult choices that will directly impact fleet capability," McFadden said in his letter to senior naval officers on both coasts.

His plan was to remove three ships from duty on the West Coast, and three others on the East Coast. Three frigates will take over their duties, sticking closer to home to pick up the slack for the ships that are slated to be mothballed.

But Gen. Natynczyk, the chief of the defence staff and the admiral's direct superior, held a news conference to reverse that order, just hours after Defence Minister Peter MacKay contradicted Adm. McFadden, saying the navy had more than enough funding to keep all of its ships afloat.

Gen. Natynczyk acknowledged that he was publicly countermanding his top naval officer in part because the government was unhappy that the cuts were made public.

"It's my job to make sure that my minister is not surprised. That's my job … I have a role to support the minister (and) we have to ensure that we meet the minister's intent," he said.

"I heard Minister McKay with regards to his guidance. But at the end of the day in the military chain of command it was my direction to rescind the order."

It was particularly embarrassing to the government because this year marks the 100th anniversary of the creation of the Canadian navy. "There's a microscope on this year," Natynczyk said. "The challenge always comes when a piece of this information rolls out and it's taken out of context."

In an interview from Ottawa with CTV's Canada AM, MacKay said the navy has another $200 million in its budget this year.

"So, in their 100th anniversary, they have record-high funding and we are in the process of building, of growth."

MacKay added that the government intends to spend billions on shipbuilding in the next two decades, largely "to increase the capability of the Canadian navy."

Marc Milner, naval expert and author of "Canada's Navy, The First Century," told Canada AM that while Ottawa could be spending more on its navy, it is also facing higher overall costs to modernize and keep its fleet in active service.

"It's entirely possible that they're spending more money, but at the moment, we're getting less bang for that buck," he said.

Milner said the navy has "major personnel problems," particularly in attracting and training new sailors.

"The navy is short about 1,400 people to man the fleet. And it's been going through a crisis really since the 1990s trying to keep people, to train them and keep them around long enough to make them into the key petty officers and combat officers that the fleet needs to operate," he said.

"It's a long, long process. You just can't pick people up off the street and make them into sailors for the navy. It's going to take probably a decade to fix the personnel problem in the fleet."

The navy is still flying elderly Sea King ship-borne helicopters, has supply and refueling ships that are in danger of rusting out and needs to refit all of its destroyers and frigates/

Natynczyk said the funding shortfalls that forced the navy to dock its patrol vessels could be made up from other branches of the Canadian Forces.

"We have to look at the (budget) allocations across the whole Canadian Forces and the Department of National Defence."

And the general insisted that his reversal of his top admiral's decision was not a vote of non-confidence.

"We are blessed to have Dean McFadden … leading the navy family, especially in this the year of the centennial of the navy," Natynczyk said. "I have the utmost confidence not only in Dean McFadden, but the flag officer, the officers, the chief petty officers and all the sailors of the Canadian navy."

With a report from CTV's Atlantic Bureau Chief Todd Battis