The Ministry of Business and Innovation says it is already working to fix problems with the way it process funding requests.
Documents obtained by Radio New Zealand News show half of the research proposals approved for a total of $227 million of government funding last year did not meet the ministry's own goals for peer review.
The ministry says it aims for each research proposals to receive three reviews from independent experts along with two reviews by end users.
But papers released under the Official Information Act show that 39 of the 79 proposals it approved received less than three reviews, 15 got just one, and some scientists complained they were given less than 24 hours to respond to critical reviews.
The ministry says the it was undergoing restructuring last year, which meant it had less time to process proposals.
Its science investments general manager, Prue Williams, says peer review is only one part of the assessment process, which is already being improved for the next funding round.
"We've changed the process for how we go about getting the science peer reviewers, we check that process from people with the sector who agreed that it was a better process to run and we've got the process underway."
The New Zealand Association of Scientists said it appears the fewer reviews a proposal received, the more likely it was to be funded.
The University of Auckland said researchers were not given enough time to respond to negative reviews.