The Conservative government is focused on treating drug addicts as opposed to making "more available access to often illegal drugs," Peter MacKay told reporters Thursday.
Earlier in the day, Coderre said the city will open supervised injection facilities — where people can inject drugs without fear of arrest — regardless of what Ottawa says about it.
Coderre said the project has been approved by city council and the provincial government. Montreal police have also been consulted.
The federal government must grant an exemption under the Controlled Drugs and Substances Act in order for a safe injection site to operate.
Quebec officially asked for the exemption at the beginning of May, but Ottawa has been publicly and strongly opposed to granting licences for facilities where people can inject drugs legally.
The only supervised injection facility in Canada is in Vancouver.
In 2011, the Supreme Court of Canada ruled that denying citizens access to safe injection sites was unconstitutional because it deprived people of potentially life-saving medical care.
In response to the court decision the Conservative government drafted a law — currently before the Senate — that imposes strict rules on the granting of licences to operate such sites.
MacKay said his government wants to ensure the communities located around proposed injection sites are consulted and "it's clear our intent is to uphold the law."
"I understand very well the law of the land," he said.
"Mayor Coderre should know that Ottawa has continually emphasized the need to consult and ensure Canadians living in these communities that would be home to these safe injection sites are given their say."
Coderre said Montreal will respect the Supreme Court decision and all other legal requirements for the facilities.
"This is not about politics, this is about health care," he said.
He added he thought Ottawa's stamp of approval "should be a formality."
Coderre wants to open a facility within a few months and suggested the federal government might stymie his efforts by delaying its decision until after the scheduled October federal election.
"There is no time to play games," Coderre said. "It's not a matter to buy time — I'm not going to fall for that. We are solid and we are going to do it anyway."
— With files from Lia Levesque