Asked if he preferred subways over light rail transit, Harper initially demurred.
"The RCMP prefers I not use any of these facilities at the present time," he quipped.
As Mayor Rob Ford looked on, the prime minister then offered what he called his personal views, saying they were based on his experiences as a commuter growing up in the city and in latter years, doing business here.
"I prefer, when I want to use public transit, to go underground unimpeded," Harper said, following an unrelated announcement at the city's island airport.
"And I prefer, when I want to use my car, I prefer not to be running into LRTs and street cars."
Even though Harper stressed that transit decisions have to be made on the ground by Toronto residents, his words are sure to offer Ford and the pro-subway contingent some powerful ammunition.
The mayor, who came to office promising a more car-friendly city, has been pressing to expand the city's subway system.
His plans have been derailed — or at least stalled — by a balky council, which has been leaning toward light rail as a less expensive option to tunnelling underground.
Last month, Ford and his allies lost a crucial battle when councillors voted 25-18 in favour of a proposal of light rail transit, instead of a subway.
Despite the loss, the mayor insisted the vote was meaningless on the grounds the province would still go ahead with his subway plan.
That prompted Premier Dalton McGuinty to say he would respect council's decision on the future of the city's transit. The province has committed $8.4 billion to the $12.6-billion transit project, with the city covering the rest.
Councillors voted for a plan to put light rail lines on Eglinton Avenue and Finch Avenue West, and to study a subway extension on Sheppard Avenue.
The province is awaiting the results of that study.
Harper's transit comments came after he turned the ceremonial sod on a 240-metre pedestrian tunnel that will link the city's increasingly busy island airport to the mainland.
Currently, airline passengers have to take one of the world's shortest ferry rides, which frequently results in bottlenecks.
The fixed link has also been a point of controversy in the city for years, with critics arguing it will spur an increase in air traffic and mean more air and noise pollution.
A clutch of demonstrators held signs at the announcement reading: "Kids need education without noise," "No fumes in classrooms," and "Say no to a public tunnel."