"That was not authorized," Harper said after being asked about the decision made public this week.
"And the (environment) minister (Peter Kent) has ordered those to be started back up again."
The controversy flared this week when the Northwest Territories minister of the environment, Michael Miltenberger, told the legislative assembly that 21 of 23 water-monitoring stations were being closed because of federal budget cuts.
"This is unacceptable, it is a slap in the face," Dene National Chief Bill Erasmus said in a release at the time.
"The federal government has obligations through land claims agreements and the government's water strategy to protect water quality and quantity."
Harper was asked about the embarrassing decision during his current northern tour. There was no immediate explanation about why federal officials made the cuts when they lacked the authority.
The controversy erupted as Harper took a helicopter tour of a glacier in Kluane (pronounced kloo-wah'-nee) National Park after stopping by a new federally funded visitor centre.
Three choppers carrying Harper and his entourage landed on an island in the glacial lake at the foot of the glacier. Rock, sand and rubble, with tiny purple flowers hiding among the boulders.
Harper seemed to enjoy the outing, asking a Parks Canada guide a lot of questions about the glacier.
It was the end of a four-day northern tour during in which Harper has repeatedly stressed what he calls the "four pillars" of his northern strategy.
But critics say environmental issues are all but forgotten by the Conservatives, who have placed a heavy emphasis on sovereignty and resource development in the Far North.
Harper's touting of a park visitor centre and a cultural centre for the Champagne and Aishihik First Nations won't likely silence the critics.
They call his annual summer Arctic foray "political tourism."
Harper says the visitor centres will attract tourists to the community of Haines Junction at the park entrance, boosting the local economy and teaching visitors about the environment and native people of the region.
"Canadians who visit Kluane will fully enjoy the natural beauty that our country has to offer and will be able to learn more about our remarkable First Nations' heritage," said the prime minister.
"The two new centres being built near spectacular Kluane National Park will give a boost to the local economy through new jobs and tourism revenues."
Asked later about competing claims in the region by other Arctic countries, Harper said Canada is working internationally to ensure Canada's territory is respected.
"The Government of Canada working with our partners, and the people in this region intend to assert our sovereignty in these regions," he said.
"We also are working co-operatively with other nations, through the United Nations Convention on the Law of the Sea, to establish various extended claims through the Arctic continental shelf and that work continues peacefully."
The prime minister was to attend Saturday's state funeral for the NDP's Jack Layton in Toronto.