Mr Trudeau said he wouldn't be 'making any more jokes' following the comment he made at a Q&A session at the MacEwan University in Edmonton.
He politely interrupted a student asking a question, saying: "We like to say 'peoplekind', not necessarily mankind."
The comment, was applauded in the room, however social media users and media reports were more critical.
Mr Trudeau addressed the criticism on Wednesday on the way to a Liberal caucus meeting.
"I made a dumb joke a few days ago that seems to have gone a little viral in the room, on the peoplekind comment," Mr Trudeau told reporters.
"It played well in the room and in context.
"Out of context it doesn't play so well, and it's a little reminder that I shouldn't be making jokes even when I think they're funny."
At the time of the comment, Mr Trudeau was answering student questions when a young woman from the World Mission Society Church of God asked whether the Canadian government could ease regulations that limited volunteering with religious organisations.
"We came here today to ask you to also look into the policies that religious charitable organisations have in our legislation so it can also be changed because maternal love is the love that is going to change the future of mankind," she said.
This prompted Mr Trudeau to ask the student to use the term 'peoplekind'.
