The Saskatchewan government is paying $40 million over four years for the program, which looks for ways to reduce spending and streamline health care.
Union president Tracy Zambory says nurses hoped that Lean concepts would be effective, but she says it's been disappointing.
"Now that Lean is being put into practice, we are seeing the primary focus is on creating efficiencies, waste reduction and budgetary savings only. It ... is unfortunately proving to have little impact on direct care at the bedside and patient outcomes," Zambory said in a statement released Tuesday.
"We are finding that Lean does not fit with the registered nursing process, safe nursing practice, registered nurse decision-making or the formulation of nursing diagnoses."
Zambory said Lean is supposed to be an inclusive process and when the largest provider of direct patient care says it's not working, "we have to go back to the drawing board."
Premier Brad Wall has defended the program. He has said it has already paid for itself with savings on two new hospital designs and with ways to reduce wait times. The premier says it's about better care and more efficiency.
Health Minister Dustin Duncan was taken by surprise by Zambory's statement because nurses had supported Lean.
Zambory said in August 2013 that there are "many commendable transformational changes" happening under the umbrella of Lean.
Duncan said he met with Zambory twice in person and spoke with her twice over the phone in the last six weeks or so and no concerns were raised.
"We have 44,000 employees in the health-care system and to get everybody to agree to anything is probably not going to be possible, but I'm a little bit surprised by the release today from SUN," Duncan told reporters at the legislature.
The health minister would not speculate on whether the statement is connected contract talks that nurses are in.
"The deputy minister of health is going to meet with SUN on Friday and so we'll explore what these seemingly new concerns are around Lean."
Lean was originally created in the manufacturing sector, but has since been applied to many other sectors and industries.
Saskatchewan is the first jurisdiction in Canada to apply the Lean program across its entire health system.