The association president, Jean Thiffault, says the government unexpectedly proposed a change that would no longer allow pharmacists to carry out some tests on site, like checking patients' blood coagulation.
Thiffault says pharmacists in Quebec have been carrying out these tests for nearly 10 years.
"The spirit of this new act is to encourage access," Thiffault told CBC's Daybreak Montreal. "[This change] is coming out of nowhere and has a significant effect on our daily practice."
The act will come into effect Sept. 3, increasing the scope of services pharmacists can offer patients, which will include assessing the need of medication for some minor health problems like cold sores, seasonal allergies and urinary tract infections.
Pharmacists will have to charge patients for services that would be covered by provincial insurance if carried out at a clinic or hosptial.
Quebec's Minister of Health, Réjean Hébert, says pharmacists will have to resume negotiations before any further amendments can be made to the act.
"The law gave [pharmacists] the ability to order a test and interpret it. Now they also want us to cover them carrying out the test, and clearly this is beyond the scope of the law," Hébert told Radio-Canada, adding that he would have to consult with professional governing bodies before making a final decision. "All this will happen around the negotiating table, so I invite them to come back."
On Wednesday, Yves Bolduc, official Opposition critic for health, told Radio-Canada that the new act would cost the province about $100 million.