The design is nearly complete, but Duncan says officials now think it may not have enough beds for the province's growing population.
"Even with what we had thought, in terms of a government, in terms of the population growth of the province, even in that time from 2009 to today, we are seeing significant growth, but as well in a specific demographic of women who are in child-bearing years," Duncan said Wednesday at the legislature.
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.
Most of the concern is around the number of beds in the maternity unit.
However, the health minister insists the design won't need to be scrapped if changes are needed.
"They're at 90 per cent in the drawings and so they wanted to stop at that point because they thought that even if additional beds were approved, that it wouldn't require a total redesign of the facility," he said.
"It would be shifting a wall, bumping a wall out, which wouldn't affect 90 per cent of the plans."
NDP Leader Cam Broten says nurses have been raising concerns about the size of the children's hospital.
He's questioning what the delay means for the cost and construction of the facility.
"My concern is how much more is this going to cost as opposed to properly designing the hospital in the first place and listening to what is needed. How much more will it cost, what are the timelines involved, what can Saskatchewan people expect?" said Broten.
Construction on the children's hospital was supposed to start early this year and be completed in late 2016.
Duncan says a final decision on how to move forward should be made in the next couple of weeks. He says one decision would be to complete the design as is and the second option would be to adds beds.
"We still are anticipating that even if there is an increased scope in the project, that we'll be able to tender the project later this year."