Queen Elizabeth II on Monday agreed to a "period of transition" while details of a more "independent" role for Harry and Meghan are hammered out. They will spend time in both the UK and Canada during this period.
The couple announced last week that they wish to step down as senior British royals and live part-time in North America.
Trudeau told a Canadian television station Monday that: "...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 and these are things that we are obviously supportive of their reflections, but have responsibilities in that as well."
Trudeau added: "That is part of the reflection that needs to be had and there are discussions going on."
Harry and Meghan say they have a "strong connection to Canada," and they spent the Christmas holidays there with Meghan's mother, Doria Ragland. The duchess is currently in the country with the couple's baby son, Archie.
Trudeau said Monday that "there is a general feeling of appreciation for the Sussexes" in Canada, but talks continue as to the exact arrangements.
"We are not entirely sure what the final decisions will be, what the dispositions are and those are the decisions for them. I think most Canadians are very supportive of having royals here, but how that looks and what kind of cost is involved, there are still lots of discussions to be had," he said.
After a crisis meeting of senior royals Monday, the Queen said she had agreed that Prince Harry and Meghan could split their time between the UK and Canada but that "complex matters" would have to be resolved.
The monarch said she had ordered final plans to be drawn up in the next few days.