Justin Trudeau said the funding and shape of the plans are to be discussed.
The Queen has agreed a “period of transition” in which Prince Harry and Meghan will be in Canada and the UK.
She said she was “entirely supportive” of their desire for a new role but “would have preferred” them to remain full-time working royals.
In a statement following talks at Sandringham, the Queen’s residence in Norfolk, on Monday involving senior royals, the Queen said she expected final decisions to be made in the coming days.
Prince Harry and Meghan have announced they wanted “step back as ‘senior’ members of the Royal Family” and divide their time between the UK and North America.
But there have been questions over who would fund their security.
Mr Trudeau said most Canadians are “very supportive” of having royals live there, but there are “still lots of discussions to have” over “how that looks and what kind of costs are involved”.
He said the federal Canadian government had not been involved “up until this point” about what the couple’s move to the country will involve.
Speaking to Global News, a Canadian television network, he added: “There are still a lot of decisions to be taken by the Royal Family, by the Sussexes themselves, as to what level of engagement they choose to have.
“We are obviously supportive of their reflections but have responsibilities in that as well.”
Earlier the Queen said the talks at Sandringham which also involved the Prince of Wales and the Duke of Cambridge, had been “very constructive”.
“My family and I are entirely supportive of Harry and Meghan’s desire to create a new life as a young family,” she said.
“Although we would have preferred them to remain full-time working members of the Royal Family, we respect and understand their wish to live a more independent life as a family while remaining a valued part of my family.”
She said it had been agreed there would be “a period of transition in which the Sussexes will spend time in Canada and the UK” after Harry and Meghan “made clear that they do not want to be reliant on public funds in their new lives”.
The urgent talks were convened after the Sussexes surprised the rest of the Royal Family last week with their statement.
They also said they wanted a “progressive new role” within the institution, where they would be financially independent.
Both Prince Harry and Meghan spoke of the difficulties of royal life and media attention in recent months, with the duke saying he feared his wife would fall victim to “the same powerful forces” that led to his mother’s death.