The Ontario Medical Association filed the application with the Ontario Superior Court, which it hopes will stop the fee cuts and order the government back to the negotiating table.
The group also wants the court to confirm its representational rights on behalf of doctors, alleging that the government threatened to go behind its back and negotiate with other physician groups, such as the College of Physicians and Surgeons.
The OMA claims that violates its members' right to freedom of association under the Charter of Rights and Freedoms and makes it "effectively impossible" for them to associate and act collectively to further their workplace goals.
The government has never tried to bypass the OMA in the 50 years that they've worked together on fees, said president Dr. Doug Weir.
"Ontario's doctors are entering uncharted waters," he said. "Not because we want to, but because we were forced there."
It was clear from the outset that the government had no intention to negotiate with them at all, he said. On the first day of talks, they were told that if they didn't comply with over a billion dollars in cuts to fees and programs, it would be forced on them.
"While we made offers, the government made threats," Weir said.
The Liberals also refused a request to bring in a conciliator, saying they were not under any obligation to negotiate with the OMA, he said.
"We cannot stand idly by while the government stomps on the rights of doctors and plows ahead with its plans to unilaterally cut $1.1 billion," Weir added.
The OMA alleges that a top ministry official indicated in April that if the OMA didn't agree to their terms, the ministry would try to engage other doctors' groups.
"He also indicated that the ministry would 'shift attention' to these organizations if the OMA refused to accept a freeze in funding for physician services," court documents state.
When the OMA asked why they were taking that position, officials told them that the constitution didn't apply to them because they weren't a trade union, the documents said.
The OMA's allegations have not been proven in court.
Health Minister Deb Matthews said she's disappointed that the OMA is taking the matter to court.
Last week, the province and the English Catholic teachers managed to reach a deal in good faith that allowed the government to meet its goals to curb costs, she said.
"I ask again that the OMA return to the table so we can move forward on a fair and reasonable outcome together," Matthews said in the statement.
Weir said the OMA is willing to go back to the table, but wants a conciliator to ensure the process is fair. The organization is not currently planning to take any other action that would affect patient care, he said.
The OMA, which represents 25,000 doctors, announced last month that it would go after the government in court in an effort to stop the rollout of fee cuts. If it wins, the OMA wants the court to order the government to compensate doctors whose fees were cut.
The government made the regulatory changes to cut Ontario Health Insurance Plan fees and premiums in May, but they're retroactively taking effect April 1.
Matthews said at the time that she was left with no choice after the OMA rejected her offer to hammer out a new four-year agreement over a weekend with a conciliator.
She said the changes will actually improve patient care, despite warnings from the OMA that it will force patients to wait longer for health care and chase doctors out of the province.
The OMA said it offered to freeze doctors' fees for two years and find an additional $250 million in savings, but Matthews rejected the proposal.
The minister said the OMA wants the government — which already spends $11 billion a year on doctors' fees — to pay for the rising costs of health care as the population ages. She wants the doctors to find the money to fill that gap.
The two sides have been battling it out since February, with the minority Liberals insisting that they can't afford any new funding increases for doctors.
They're demanding a wage freeze from all broader public sector workers, including teachers, nurses and civil servants. They've threatened to legislate the pay freeze if all other options at the negotiating table fail.
The Progressive Conservatives have been pushing the government to legislate the freeze immediately to save money. But Tory Steve Clark took a softer line Monday, saying the government must restart talks with doctors.
"We've called for a mandatory freeze," he said. "Certainly we'll take it however we can get it."