The medical society launched a challenge of the government's planned $20 million cut and subsequent $425-million cap to annual medicare payments.
But Judge Judy Clendenning of the Court of Queen's Bench said the application to the court was only for a declaration on the agreement.
"Consequently, the issue of a cap being imposed is not at issue in this application," Clendenning wrote.
Health Minister Hugh Flemming said the decision doesn't change anything.
"I don't see the decision doing anything other than stating the obvious that we have a valid and binding agreement — something that I've always acknowledged," he said.
Flemming said the cap has not been used and medicare billings are below budget during the first quarter of this year.
He said he hopes the medical society will meet soon to look for other ways to help control health-care spending.
Medical society president Dr. Robert Desjardins said his group got what it wanted in the ruling.
"I hope that this judgment will just send a signal to the government that we have to sit meaningfully at the negotiating table, and we have to build trust between the government and the medical society," he said.
Desjardins said the society offered to drop the court case last week if the government would sign a court order acknowledging their agreement was binding. But that was rejected.
While the government has yet to actually cap any medicare billings, Desjardins wouldn't say what his group would do if that happened.
"We cannot at this time speculate of what we will do if the cap is indeed used," he said.
Desjardins said he hopes negotiations with the province for a new fee agreement will resume in the near future.