Spokesman Dale Burgos says it was the principal at Sisler High School who enforced a media ban, because students had not signed waiver forms allowing them to be filmed.
Burgos says Trudeau's appearance on Thursday was never intended for the media and the principal was not aware ahead of time that reporters were planning to attend.
Media were told minutes before Trudeau's talk with students that word had come down from the school division and they had to leave.
Trudeau blamed "petty politics" for the decision.
Other politicians have had media events at Winnipeg schools, including a recent funding announcement by Manitoba Premier Greg Selinger, but Burgos said students had signed waivers in that case.
"We'd been working with the province on that, finding a school and making sure that the students that are in the gym at that time had all signed (waivers) and that they're safe to be photographed and filmed," he said.
Students in the division sign general waivers allowing themselves to be filmed at the start of the school year, Burgos explained, but the division's practice is to have waivers signed for each specific event.
"There's a consent form that I tailor for every event ... and that wasn't created (in Trudeau's case)."
The Trudeau kerfuffle generated a lot of online discussion about whether politicians should hold media events in schools.
A message from a Twitter account under the name of Suzanne Hrynyk, a Winnipeg School Division trustee, said "schools should not be used as political conduits for any elected official."