Health Minister Gaetan Barrette has been pulled from negotiations with the province's medical specialists.
Negotiations over Bill 130 have been tense.
The legislation gives hospitals and health centre directors the power to force doctors to work at night an on weekends.
The federation was planning to go to court this week to fight the bill, but a call from the Premier got them to reconsider.
"This morning the premier informed me that he will now take over in our negotiation of our working conditions," said Federation president Diane Francoeur.
The FMSQ said it has been assured that Barrette will no longer be at the negotiating table.
Barrette did not comment on the decision.
With files from CTV Montreal