Professor Hendy claimed Crown research institutes were increasingly under pressure to find private funding, so had tight, corporate-like policies filtering what scientists could say to journalists.
"This is not to say that publicly employed scientists shouldn't work with the private sector, but in a science community that is as thinly spread as New Zealand's, it can mean that in times of crisis we simply run out of experts who are free to speak."
He proposed a Commission for Science, responsible to Parliament rather than the Government, which could investigate complaints from whistle-blowers and increase transparency.
But Science and Innovation Minister Steven Joyce rejected the notion scientists were being muzzled, saying the only potential issue was where contracted research was involved.
"In general terms, you'd have to say New Zealand has a very robust scientific communication environment; there are lots of issues that scientists speak on, as they should, and they get the opportunity to do so."
In discussions with the research community about new potential guidelines around public engagement, the Royal Society of New Zealand found only a few comments around constraints, president Professor Richard Bedford said.
Mr Joyce said a commission was not needed, arguing the interests of science and scientists were already served by the democratic process.
The Prime Minister's chief science adviser, Sir Peter Gluckman, said New Zealand had a strong science advisory system, with groups such as the Parliamentary Library and the Royal Society, which he described as "fiercely independent" of Government.
His own role was independent, he said, but was largely around providing evidence for policy, "rather than policy for science".
"Science, policy and society is a three-way thing: science does not make policy, and in fact the worst thing we can do as scientists is exhibit hubris and think we know what policy-making is all about."
