Video report by ITV News Royal Editor Chris Ship
This has raised questions about who will pay for Meghan and Harry's security once the move is complete, among other financial decisions.
In an interview with Global News Canada, Mr Trudeau said "most Canadians are very supportive of having royals" in the country, but "how that looks and what kind of costs are involved, there are still lots of discussions to have".
Asked whether Canadian taxpayers may have to foot the bill, he added: “That is part of the reflection that needs to be had and there are discussions going on.
“We’re not entirely sure what the final decisions will be, what the dispositions are and those are decisions for them."
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.
“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,” Mr Trudeau said.
“We are obviously supportive of their reflections but have responsibilities in that as well.”
The Sussexes enjoyed a “general feeling of appreciation” in Canada, he added.
Back at home, the monarch, Prince William, Prince Charles and Prince Harry met at the Queen's Sandringham estate in Norfolk, but it has been confirmed by Buckingham Palace that Meghan did not dial in from Canada.
A palace aide told ITV News Royal Editor Chris Ship "it wasn't necessary".
The earlier indication was that the Duchess of Sussex would join the family meeting by phone from Canada.
She flew back to Vancouver Island last week, where she joined baby Archie, who was still in Canada.
Prince William was seen on the school run, leaving Kensington Palace on Tuesday morning.
He is presenting investitures at Buckingham Palace later on Tuesday, including to former England cricket captain Andrew Strauss, who is to be knighted, and singer MIA.
While Camilla, the Duchess of Cornwall, presented her sister-in-law, the Princess Royal, with an honourary degree at the University of Aberdeen, in her capacity as chancellor.
Princess Anne received the honorary degree of Doctor of Laws for her charity work and contribution to sport.
Canada’s finance minister Bill Morneau told reporters in Toronto that the government “had not spent any time” thinking about the couple’s security costs.
In her first public comments since Meghan and Harry released their bombshell statement last week, the Queen expressed her regret at their wish to step back as senior royals.
But she said her family “respect and understand” their wishes for more independence while still remaining a “valued part” of the monarchy.
In an unusual move, Harry and Meghan were not referred to as the duke and duchess in the statement, only as the Sussexes and by their first names, raising questions about whether they will retain their titles.
The Queen was joined by the Prince of Wales and Duke of Cambridge for “very constructive” face-to-face talks with Harry at her private Norfolk estate.
The head of state also expressed the “support” of herself and the rest of the family for the couple’s aspiration to create a new life together with their eight-month-old son Archie.
She stressed the discussions were “complex matters” for her family to resolve but she wanted “final decisions” in the “coming days”.
Harry and Meghan made clear in their statement last week they wanted to step back from being senior royals, become financially independent and split their time between North America and the UK.
In another development, William and Harry made a joint show of strength by issuing a statement denying a newspaper claim about their relationship, which they branded “offensive and potentially harmful”.
The statement did not name the newspaper but The Times had a front page story about the crisis, and said a source told the publication Harry and Meghan “regarded themselves as having been pushed away by what they saw as a bullying attitude from the Duke of Cambridge”.
A number of questions remain unanswered, with the central issue being how the Sussexes will fund their future lives and whether any deals will have to be scrutinised by the palace.
The Royal Rota: Harry, Meghan and the Sandringham summit