About 60 people from the Lake St. Martin and Little Saskatchewan First Nations have been staying at the Misty Lake Lodge in Gimli after flooding in 2011.
But the owner has said the Manitoba Association of Native Firefighters has not paid for all of their lodging.
Michael Bruneau plans to close the business next month because he can't afford to keep the doors open.
The Manitoba and federal governments issued a joint statement late Tuesday, saying they will continue to supply shelter, food and other services to evacuees as required.
The firefighters' association is being audited by the federal government. (CJOB)