The company said it budgeted $1 million per year to operate the water treatment system. They say it now costs them more than $4 million to run.
So far, there's no word from federal regulators about what they'll do, and that's a concern for environmentalists.
"Who now then is responsible for it? Is it the Federal government? Is it the provincial government? Is it the company? It seems to be very unclear" said Lewis Rifkind, the mining co-ordinator for the Yukon Conservation Society.
The mine runs near the Taku River, which is home to many fish species including salmon.
The company said it is trying to find ways to make the system more efficient. But until it does, it said it will shut down the system and won't be able to comply with federal regulations.