Duncan said more beds will be added and the overall size of the Saskatoon-based hospital could grow too.
"Essentially what will take place is, because this isn't a rewrite of the entire plans, basically a wall will be shifted, that changes the footprint," Duncan said Thursday at the legislature.
He said the cost of the hospital will be announced next week.
"There will be an increased cost based on the number of beds that is being proposed, but this doesn't change any of the planning dollars that have been already provided for the project," he said.
A detailed design was unveiled with great fanfare in April 2013 after the project team spent eight months working on the layout with staff, physicians and families.
Duncan said Wednesday that the design for the children's hospital was 90 per cent complete, but was on "pause" because officials now think it may not have enough beds for the province's growing population.
He said the design was based on 2009 population projections, but that growth has been higher than first thought, especially in the number of women who are in child-bearing years.
Most of the concern is around the number of beds in the maternity unit.
He said Wednesday that a final decision on how to move forward was pending. He said one decision would be to complete the design as-is. The second option would be to adds beds.
Construction was supposed to start early this year and be completed in late 2016. Duncan said construction will now start in September.
NDP Leader Cam Broten wondered why the minister changed his story.
"In committee, in speaking with the media, he was saying 'Well, they're just looking at this, there's no plan yet.' He was very vague on the details," Broten said Thursday.
He said the situation drives home the point "that this government will do whatever it can to have some sort of ceremony where they can cut a cake, but won't actually be clear on the plans."