Bob Pringle said Ottawa provided the money to bands, which used the cash to contract services through the province's Early Childhood Intervention Program.
That funding is to be cut at the end of June, he said.
"What the bands are concerned about is that they're already short funding," Pringle said in an interview Tuesday.
"So if they lose this federal money for the Early Childhood Intervention Program for children in their communities, they're going to have to take money from existing funds to fund these services if they want them to continue, but it will not be from this pool of 1.2 or whatever million dollars."
The program helped young children with developmental delays prepare for school.
Staff also organized medical outreach clinics and brought specialists to the North so that families didn't have to travel hundreds of kilometres to Saskatoon.
"We understand that is in jeopardy because the specialists are indicating that there's no point in providing a diagnosis yet, if there's no one there to provide the service," Pringle said.
The advocate said program staff worked with 159 children living on reserves last year, but he added there are many more who need services — if there were more money.
Pringle said cutting the funding runs counter to the idea of giving children a good start in life.
"We should be expanding the support to make sure that children on reserve are school-ready, but also that children have a right to equal services no matter where they're living in the province."