"It didn't seem to me that the premier was quite as aware of our worldwide obligation to the U.N. Convention on refugees as he might have been, so I spent a little time explaining how the asylum-seeking system works and how our system is supposed to operate", Trudeau said.
Trudeau said Ford had a number of questions about immigration issues during their closed-door discussion.
On Friday, Lisa MacLeod, Ontario's minister of children, community and social services, fired back at Trudeau saying if he's going to continue to encourage people to seek refuge in Canada, his government should foot the bill.
The federal government has allocated $50 million for the provinces of Ontario, Manitoba and Quebec, where more than 7,600 illegal asylum seekers crossed into Canada from the U.S.in the first four months of 2018. "This mess was 100% the result of the Federal Government".
"If (Trudeau) wants to welcome them in, that's fine, but he should make sure that he's paying for them", MacLeod said.
"The premier and I talked directly about the fact that we have very clear mandates from the people who elected us", he said.
But another fight is brewing over Ford's decision to scrap the cap-and-trade program, in part to lower gas prices, putting him at odds with the federal government's plan for carbon pricing across the country.
A surge of asylum seekers from the United States has caused strife between Canadian Prime Minister Justin Trudeau and the leader of the most populous province.
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Quebec alone estimates their cost at about $146 million because they rightly include ongoing costs for housing and settlement, yet they're only in line for about $36 million. On Thursday, the province withdrew its cooperation with Ottawa on the resettlement of asylum seekers, seemingly bringing an end to a previous agreement wherein Ontario committed to helping resettle some refugees.
Tory has previously said the city has run out of space, resources and people to help settle asylum seekers, and called for other governments to help.
"The response that I got from across Ontario was fabulously positive and they've agreed, many of them from different parts of the province, to help", Tory said, adding numerous mayors suggested they also had jobs to offer newcomers.
Toronto is now housing some 800 migrants, including 200 children in dormitories at two Toronto colleges - a temporary solution that will end in August when students return to school.
The federal government has already earmarked C$11m ($8.4m; £6.3m) to help Ontario with housing asylum seekers, but Mr Tory said he needs more like C$64m.
Ford spokesman Simon Jefferies said the premier is making good on a promise of his own made during the spring provincial election campaign.
"Over the past year, we have also worked closely with Quebec to ensure that adequate resources are in place and that every action is taken to reduce the impacts on provincial social services".
Meanwhile, some of those tasked with helping to house the newcomers say the disagreement between Ottawa and Ontario over the issue has left them in limbo.