It came after what Research, Science and Innovation Minister Megan Woods described as a "positive" mid-way performance review by the Government's Science Board.
Woods said the review – which didn't compare the individual challenges but assessed the progress of each – had shown the challenges were "fundamentally changing the way science is being undertaken in New Zealand".
The Ministry for Business, Innovation and Employment (MBIE) provided the Herald with a summary of the review, which stated the challenges were delivering collaborative programmes, supporting "excellent science" and had "appropriate governance and decision-making processes".
However, MBIE has withheld the full review, prompting the Herald to request it under the Official Information Act.
MBIE's strategic investments manager Danette Olsen said the ministry did not release assessment or peer-review reports that supported investment decisions made by the Science Board.
"This empowers reviewers and experts to provide their free and frank advice, and also protects potentially sensitive information and intellectual property."
The New Zealand Association of Scientists (NZAS) was "extremely concerned" that MBIE was keeping the full review secret.
"This is public funding used for the national good," president Dr Heide Friedrich said.
"The NZAS would welcome for review information to be made public, and thus contributing to a healthy discussion on research funding mechanisms."
Friedrich said the association was concerned the review asked the right questions, given the new funding had come without changes.
"Should we have seen adjustments or indeed more substantial changes to the detailed distribution of funding, taking into account what we have learned over the last five years?
"The NZAS has also concerns about the cost of governance - could we have achieved more with the funding through existing funding pathways?"
Science commentator and past NZAS president Professor Shaun Hendy was also critical of the process.
"Normally, scientific reviews of research programmes like these would be kept confidential, but the public were important stakeholders in the challenges and even played a role in selecting them," he said.
"I think the lack of transparency in the selection of the challenges by the peak panel, particularly where this deviated from the popular voting, demands a higher level of public scrutiny than we might ordinarily ask for."
Hendy said there had been some wins from the challenges – more than 150 projects were underway, delivering more than 400 publications since 2014 – they had also put an "extraordinary level of stress" on the science system.
"There has been a lot of discussion about the resource that is going into their governance for instance," he said.
"Furthermore it would be very helpful of we had some public data on who is being funded and for what.
"Right now, it's very hard to tell whether the challenges are engaging with emerging researchers or whether, as some of the criticisms have suggested, the funding is going to an old boys' network."
Another prominent scientist, MacDiarmid Institute co-director Associate Professor Nicola Gaston, said one of the biggest concerns around the challenges and their funding was an original indication they would provide a "de facto science strategy" for the country.
But Gaston said the development of the Government's National Statement of Science Investment had gone some way to removing concerns around funding, as it had made clearer the relationships between different parts of the sector.
"However the balance between complexity and efficiency of our research system is a delicate one that does need monitoring — for now I would say that the stability provided by this continued funding is absolutely what the sector needs."
Hendy still wanted to see a tough audit of the way the challenges were selected, procured and contracted, "so we can figure out how this might be done better in the future".
The 11 challenges are "A Better Start", "Ageing Well", "Building Better Homes, Towns and Cities", "Healthier Lives", "High-Value Nutrition", "New Zealand's Biological Heritage", "Our Land And Water", "Resilience To Nature's Challenges", "Science for Technological Innovation", "Sustainable Seas" and "The Deep South".
The largest amounts in the second round of funding went to Science for Technological Innovation, Our Land and Water and High-Value Nutrition, which received $72.7 million, $69.3 million and $53.2 million respectively.
MBIE planned to release summaries of reviews of each of the challenges next week.
