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Loose housing wrap blows in the breeze on the Lake St. Martin reserve in Manitoba on Oct. 31, 2012. Since a flood in spring 2011, Lake St. Martin has been declared uninhabitable and officials have been working to find the First Nation a new home.FRED LUM/The Globe and Mail

Manitoba is calling on the federal government to invest heavily to flood-proof reserves as the cost of caring for hundreds of aboriginal flood evacuees tops $90-million.

Emergency Measures Minister Steve Ashton says Ottawa should spend millions upgrading chronically flooded native land to save money down the road. Many First Nations were historically moved onto a flood plain and should be better protected, he says.

"First Nations are chronically underfunded when it comes to infrastructure," Ashton said in an interview. "If you are looking at a longer-term fix … you're into the tens of millions of dollars. But the alternative is what we've seen where, year after year, those First Nations are impacted by flooding."

About 2,000 aboriginal people are still out of their homes almost three years after heavy flooding in Manitoba in spring 2011. The $90-million cost so far is borne by the federal government.

Most evacuees are living in hotels and temporary housing scattered around the province. At least one reserve, Lake St. Martin, has been declared uninhabitable and officials have been working to find the First Nation a new home.

A Red Cross study found many flood refugees are on an "emotional roller-coaster" and are adjusting poorly to life in urban Winnipeg.

It costs the federal government about $1.5-million a month to provide food and shelter. That money could have been better spent upgrading the communities so homes were safe from flood waters in the first place, Ashton said.

"The federal government itself is 100-per-cent responsible because of its fiduciary relationship with First Nations," he said. "It makes sense, most importantly for the human side, to make sure people don't have to go through the trauma of flooding – but [it] also makes sense financially."

Erica Meekes, press secretary for federal Aboriginal Affairs Minister Bernard Valcourt, said the minister wasn't available for an interview.

"The health and safety of First Nation communities is a priority for our government, including timely, effective and efficient support in times of emergency," Valcourt said in an e-mailed statement.

"That is why we are taking action to ensure that all residents of First Nation communities receive emergency services comparable to those that protect every other Canadian. We will work with provinces and territories to support stronger and more resilient First Nation communities."

Valcourt was in Winnipeg in November to announce that Ottawa is streamlining how disaster relief is delivered to aboriginal communities so they get funding more quickly. He also said the federal government was spending $19-million to help them with emergency preparedness.

Grand chief Derek Nepinak with the Assembly of Manitoba Chiefs did not respond to several interview requests. Manitoba regional chief Bill Traverse, who is with the Assembly of First Nations, couldn't be reached for comment.

One month ago, Premier Greg Selinger said Lake St. Martin evacuees were close to getting more permanent housing. In mid-December, Selinger said the province identified new land for the reserve and has an agreement in principle with the federal government that could be finalized soon.

Nothing has been announced.

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