The province's estimates say the budget for the agency has been reduced to $669,500 from last year's level of $848,400.
John Walsh says this means that three positions will be cut from the staff, including two administrators and a lawyer.
Walsh also says the ability to provide education programs and to mediate human rights claims will be largely eliminated.
The commissioner says the agency will still be able to conduct public hearings, but it is likely that waiting periods will increase.
"Once the figures were released we knew we'd be severely impacted," he said.
"It's really unfortunate and in our view obviously it's a little regressive."
A spokesman for the provincial Justice Department says the minister is unavailable for comment about the impact of the cuts.
The premier has said that the province's forecast debt of $9.5 billion means that cuts to government-funded positions are necessary.