It will be the third year the centre will show a deficit, says director Jakob Gearheard.
In 2003, the Nunavut government cut the funding which paid for daily administrative and operational costs, he says.
At that time, former director Tracy Thomas said she planned to approach the GN department of Health and Social Services.
Gearheard says the money problems still exist, but he did not know the exact amount of the total deficit.
A portion of the centre's programming budget can be put towards daily expenses, but each year the centre still falls short of the $250,000 required for operation and maintenance, he said.
"What we need is somebody to recognize the significance of what we're doing here in Clyde River," says Gearheard.
Open for about 10 years, the centre runs numerous community wellness programs, including a family counselling service, mens and womens healing circles, and the community's only addictions counselling service.
"It's a safe place to bring young children," said children's programming director Georgina Illauq, one of about 50 full- and part-time employees.
In total, about 30 programs at the centre are individually funded by a variety of agencies, said Gearheard.
The departments of Health and Social Services and Education, along with Health Canada, still make large financial contributions to projects and programs being run at the centre, Gearheard said.
Gearheard said the departments have expressed an interest in helping the centre meet its daily financial needs, but he has yet to meet with them.
The centre is not in immediate danger of closing.
Calls to the Department of Health and Social were not returned before deadline.