About 25 trainees have been placed, but programme director Dr Sue Adams said that many were "waiting in the wings" or had been stymied due to the pandemic "drastically" delaying getting placements up and running at community providers.
"Those folk we will not be able to see the true fruition of their success if we can't roll over that funding," Adams said.
"And the funding is there to do that."
Ministry chief nursing officer Lorraine Hetaraka said the advice to the school was the "funding should continue to be used for the purpose of the contract", which ends in December 2024.
But Adams said they "don't want to spend it now", as some nurses had been forced to take a year or two out due to pressures at their regular jobs.
"We want to spend it on those nurses who are committing to becoming enrolled nurses or nurse practitioners in the future," she said.
Hetaraka said the ministry would work to ensure any concerns about continued support for the nurses in the programme "will be addressed once the current contract finishes".
Adams labelled it a "nothing response" and inaccurate in that it suggested the underspend was only on enrolled nurses, when it was on nurse practitioners, too.
However, she said the school hoped that Hetaraka had said it appeared more Māori health workers (kaimahi) were interested in training to become enrolled nurses under the programme.
That seemed to signal they could use the underspend there, Adams said.
The University of Auckland programme laid out its case in a five-page letter in April that said the pilot programme was being targeted at "often very small community providers" and beginning to return "enormous benefits".
Read the letter in full
This included placing four Māori and one Māori/ Pacific enrolled nurses with rural Māori populations, at a time when very few enrolled nurses worked in primary health care.
Forty Māori registered nurses were already in or wanting to start the nurse practitioner training: "Ideally, we need to support all these NPs [nurse practitioners] as they transition into practice ... and this is beyond the end date of the contract."
But the pandemic's "particular and significant delays have been in working with Māori, Pacific, and other small community health providers ... [they] just do not have the space in the current climate to develop a plan for their nursing workforce".
The school asked not just for the rollover into 2025, but for the health reforms to back the programme long term.
The ministry and Health NZ Te Whatu Ora are drawing up an interim two-year plan for all health services nationwide, which they promised to release soon.
Adams said she had "no idea" about the plan or how to engage with it, and had checked with others in nurse training who said the same.
They had also been expecting the chief nurse's office, which had been "incredibly supportive", to release a nursing strategy.
Adams questioned if the chief nurse's office was being marginalised.
"All in all" the new centralised health authorities "have been far removed" from the frontline, she said.