The move offers an early example of the pro-independence Parti Quebecois government working to lessen political ties to the rest of Canada.
The decision, which was made public on Monday, was quietly announced in a letter dated Jan. 11 and signed by Health Minister Rejean Hebert and Intergovernmental Affairs Minister Alexandre Cloutier.
The working group was set up in January 2012 to look at improving how health-care services are delivered and how to better manage resources.
It is operated under the Council of the Federation, an interprovincial body first created by former Quebec premier Jean Charest, a staunch federalist.
Premier Pauline Marois has actually continued to participate in the council, surprising some of her own supporters. She is scheduled to meet with the party's rank and file at an upcoming convention.
News of the withdrawal from the health group came as Cloutier testified Monday at a committee looking at spending estimates.
He came under fire from critics from the provincial Liberals and Coalition parties, who said it was contradictory for him to hold the dual portfolios of intergovernmental affairs and minister of sovereigntist governance.
"The minister of intergovernmental affairs is mandated to ensure the proper functioning of the federation and Quebec within the federation," said Coalition spokesman Eric Caire. "I would think that the mandate of the minister of sovereigntist governance would be the contrary."
Both Caire and Liberal Pierre Moreau said they were worried that Premier Pauline Marois would use public money to promote sovereignty although Cloutier said that so far no taxpayer dollars had been used.
Cloutier also said his two jobs are perfectly compatible.
He also said the Parti Quebecois minority government has no plans to hold a referendum on sovereignty, but added, "That does not mean that we will sit with our arms folded."