Bernard Valcourt says the measure is effective as of Wednesday.
In a news release, Valcourt says the government wanted to make sure things were in order prior to "the upcoming flood season."
He says the deal ensures that First Nations have support for any potential evacuations this year due to flood, fire or other circumstances.
Aboriginal evacuees used to be the responsibility of the Manitoba Association of Native Firefighters but late last year the federal government pulled its funding and said it would not renew an agreement with the controversial organization.
The association had been given millions to care for flood and forest fire evacuees but was audited by Aboriginal Affairs and Northern Development Canada after allegations were made about money being squandered.
Earlier this year, the Red Cross was put in charge of the long-term care of about 2,000 people evacuated from reserves around the province in 2011.
Many have never been able to return to their homes and have been scattered around Winnipeg and other parts of the province while officials try to find new and long-term housing.
The Red Cross says it will contribute $500,000 on its own to train and deploy 250 volunteers to assist with First Nation evacuations.
"The health and safety of First Nation community members is a top priority for our government," said Valcourt.
"I am pleased that the Canadian Red Cross has agreed to provide evacuation services for First Nations in Manitoba this year."