Andrew Swan says federal cash runs out next year for the court which helps turn lives around through supervised rehabilitation.
Swan says it costs Ottawa $600,000 a year, but the Conservative government won't commit to a funding extension.
Associate Chief Judge John Guy says the court, which is believed to be unique, is facing an uncertain future.
He says it takes up to two years for people to complete the program and it is hard to admit new participants without long-term funding.
A spokeswoman for the federal Justice Department would only say discussions about the court's funding are ongoing.