Mayor John Tory "wants more information" from the federal government about its decision to scrap the Public Transit Tax Credit in Wednesday's budget.
The credit was worth about $200 for those who pay upwards of $113 per month for transit.
In announcing the move in its latest budget, the government said the credit was "ineffective in encouraging the use of public transit and reducing greenhouse gas emissions."
Don Peat, spokesperson for Tory, said the mayor is "very concerned" about keeping transit affordable for residents.
"The mayor wants more information from the federal government about why that public transit tax credit decision was made," Peat said in a statement to CBC News.
"One of the arguments we've heard so far is that there was low uptake on the credit. The mayor has also asked TTC staff to try to determine the impact of what eliminating this tax credit would mean for our transit system."
TTC spokesperson Brad Ross would only say Thursday morning that staff will conduct an analysis and "likely report back to the TTC board at its next meeting."
Asked about the move during an event in Toronto Thursday, Prime Minister Justin Trudeau said investing in new transit lines and bus routes and generally improving service is more important for Canadians.
"The issue with the tax credit is that it was very complex, there was extremely low take-up and the money is better spent actually investing in better opportunities for more people to take transit," Trudeau said.
Asked to respond to Tory and other critics who say eliminating the credit is a disincentive to taking transit, Trudeau said not everyone has the option of driving to work.
"We know that investing in public transit; investing in reliable, safe and regular public transit that responds to the needs of Canadians who have to get to school, to work and get home in time to care for their kids and have a quality of life, is essential," the prime minister said. "And that's exactly the focus we've made in investing in the right kinds of things that are going to create those greater opportunities for communities, for citizens and for economic growth."
The federal budget included $20.1 billion over 11 years for transit projects across the country.
'There's no point in taking it anymore'
While Trudeau suggested that low uptake was partly responsible for the decision to scrap the credit, transit riders in Toronto Thursday were disappointed.
"Commuting is not easy: limited seating, [being] shoved, pushed, you're bound by schedules, they're late. And the only tax break that the 'Working Joe' has is 'Okay, I can put it on my income tax and now I can't do it anymore,'" Rose Clavet told CBC Toronto's Linda Ward at Union Station.
Clavet said the credit helped reduce her burden at tax time, which means she will have to re-arrange her budget. The decision will also encourage her to drive and park downtown, she said.
"There's no point in taking it anymore," she said.
David Lord, who commutes by GO Transit every day, said with transportation costs going up, he will work from home more.
"I always thought the break was a good thing," Lord said. "We're getting squeezed every penny that we have and that we're earning right now."
Ontario Finance Minister Charles Sousa, himself expected to hand down a provincial budget soon, said Thursday that he could not speak to the federal government's reasoning behind the decision. But he told CBC Radio's Metro Morning that "we need to provide support and encouragement" for public transit use.
Asked whether he would consider bringing in a similar credit in his next budget or provide relief in another way, Sousa would only say he is considering his options.
"I've haven't taken a look at a tax credit specifically for the use of public transit, but I am looking at ways to make it easier and more effective to use public transit," Sousa said.