The Ministry of Social Development did not renew the contract for the Growing Up in New Zealand (GUiNZ) project at the end of February.
It told RNZ a decision on funding for the research, which has tracked more than 6000 children since 2009, now lies with government ministers.
Social Development and Employment Minister Louise Upston told RNZ in a statement: "The coalition government values the work that the Growing Up in New Zealand study has produced over time, and we would like to see it continue."
"We are considering options for ongoing funding of the study and will be making decisions on this in due course."
The contract was not renewed even though last year's government Budget included $30 million over four years to continue the study.
That allocation provided annual sums of $10.8 million, $7 million and $11.7 million, and finally $344,000 for the 2026/27 financial year.
The University of Auckland told RNZ the Ministry of Social Development (MSD) was the main funder of the study.
"MSD has not made any decisions regarding the ongoing funding of the study beyond February 2024, when the most recent contract and funding ended," it said.
"The University of Auckland is committed to ensuring the continuation of this important longitudinal study and, as such, the university's Faculty of Medical and Health Sciences will be responsible for ongoing management of GUiNZ. The university is exploring options for ongoing funding to support the GUiNZ research."
MSD deputy chief executive strategy and insights Sacha O'Dea said the study had received $80 million in government funding since it started.
"The most recent contract expired at the end of February and at this point we have not confirmed a further contract as it is subject to decisions by ministers."
Developmental and community paediatrician Jin Russell completed her PhD studies using data from the Growing Up in New Zealand study.
She told RNZ the study was "an incredibly rich resource" that would become more valuable the longer it continued.
"I'd be really supportive of the government continuing to fund this study," she said.
"The longer the study is funded to keep going, the richer the data that's coming out of it and the richer the insights that researchers like me can draw," she said.
Russell said the study was New Zealand's largest and most diverse study of children and their families and the subjects were now 14 to 15 years old.
"We're starting to get insights directly from young people themselves about their schooling, their health, their wellbeing, their mental health," she said.
"We're able to look back across their entire lives, from before they were born, to understand what is influencing their development, their wellbeing, their vision for the future. We're able to draw insights in a way that no other study in New Zealand can provide for us."
The Growing Up in New Zealand project describes itself as New Zealand's "largest contemporary longitudinal study of child development".
It monitors the participating families every two to three years and started gathering information before the children were even born.
The project has reported on subjects including disadvantage for Māori children, the effect of disability, depression and anxiety, puberty, housing and homelessness, and food insecurity.
It was not the first time the study has had funding problems.
A National government reduced its funding by $2 million so it could work with only 2000 children, but the incoming Labour-New Zealand First government reversed that decision in 2018.
The current uncertainty over funding for the study comes amid wider fears about science funding.
The government cancelled its predecessor's plans for a $451 million spend on science infrastructure in Wellington and recently announced two advisory groups on science funding and university funding.
Both groups would be headed by Prof Sir Peter Gluckman, who was chief science adviser to the Prime Minister from 2009-2018.
