John Tory — a former Ontario Conservative leader — said Friday he sat down with Harper for a brief meeting at Toronto's Pearson International Airport.
Harper was in the Toronto area for a pre-budget roundtable discussion with the Retail Council of Canada.
Tory said they talked about transit in the city, jobs, the economy and housing.
But he did not comment specifically on Harper's relationship with Premier Kathleen Wynne, saying his focus was on his job as Toronto's mayor.
Wynne last met with the federal Conservative leader on Dec. 5 of last year and sent him a letter this week, saying it's been too long since they got together.
In the letter, which Wynne released publicly, she said their relationship should be one of "collaboration, not confrontation."
Wynne also wrote that some of her ministers have reached out to their federal counterparts on issues she raised in previous letters to Harper, but added that is "no substitute for leadership and collaboration at the top."
Harper and Wynne have publicly disagreed over pension plans, infrastructure and transit.
Tory said Friday that it's important for him to keep an "excellent relationship" with Ontario's government, the premier and her ministers.
"You take these political relationships one step at a time and one day at a time," said Tory.
"I've got my job to do and I'll be trying to use in a productive way the relationships I have and to hopefully make the partnerships between all three governments work better."
Also on HuffPost