Cecil Clarke said Monday he was informed of the change in services by Local 1995 of the Nova Scotia Government and General Employees Union, which represents officers with the Cape Breton Regional Police Service.
Clarke said the union argues the municipality did not provide adequate legal support for an officer who was convicted of breach of trust and obstruction of justice.
The municipality also said the union has taken issue with the fact that the officer's pay was suspended during the legal process.
"I regret the union has decided to take a matter that was before the courts and something that was not previously brought into the collective bargaining process that I've been a part of, and choose to make a decision to step away from other services that are imperative to public safety and policing services," Clarke said in an interview.
Union president Joan Jessome said the issue has been simmering for some time.
"They don't feel they have adequate protection, legally, in the event that an officer is charged with wrongdoing," she said. "The case that the mayor is referring to may be the catalyst ... but at the end of the day, this issue is not new."
Jessome said there are about 180 active police officers in the union local.
"We're looking at trying to negotiate something that would bring this to an end that both sides would be comfortable with," she said. "We're not there yet."
Clarke said 48 positions in four special police units are affected by the withdrawal, including the force's emergency response team, the public safety unit, the training unit, and the dive team and marine unit.
He said officers have different responsibilities depending on the unit. The emergency response team, for example, could be called into action during a standoff, while members of the public safety unit sometimes act as security during large public events.
Clarke said he has ordered police Chief Peter McIsaac to request the RCMP's assistance in providing the services if necessary.
Provincial Justice Minister Lena Diab said her office has been in contact with the regional police service and the RCMP to ensure public safety is maintained.
"I have no reason to think public safety is at risk," she said.