Lean came under fire when the government rolled it out across the health-care system as a way to cut costs and promote efficiency.
Education Minister Don Morgan said Lean training is available to school districts and participation is entirely voluntary.
He added the program is being used to streamline administration and savings will "free up" money for the classroom.
"Most of the money that our ministry spends goes out to the divisions," he said. "Where you look for efficiencies is in how you acquire school buses or relocate classes, how you do payroll, how you do human resources."
Government spokeswoman Kathy Young said $33,000 was spent on Lean in education in 2014-15, with around half of that coming from school divisions and the rest from government. She added that there are two full-time employees in the ministry to support Lean work and no dedicated funding to Lean in the ministry's budget.
She said Lean has helped to save $100,000 in the teacher certification process.
NDP education critic Trent Wotherspoon said the government is urging school districts to divert funds away from students and instead put the money towards Lean.
"We know that the resources for the school divisions across Saskatchewan are already inadequate," he said. "We know that classrooms are overcrowded and under-resourced and that students don't have the supports they deserve."
He added that Lean should be scrapped before it's rammed through the education system.
"We need to recognize that Lean may have a solid place in manufacturing processes but there is a big difference between kids and cars. A car can be recalled, a kid can't," he said.
The NDP has repeatedly criticized the Lean program in the province's health-care system and said it meant injecting funds into a bloated administration that hurt front-line workers.
Opposition leader Cam Broten criticized a $40-million contract with U.S. consultant John Black and Associates, including how money was allocated to travel expenses and Lean training exercises.
That contract ended last month and the government has continued to champion Lean as a way to save money and improve health care.
Health Minister Dustin Duncan has said Lean has resulted in $125 million in savings, including day-to-day operations and the design for a new hospital in Moose Jaw.