Speakers at a major science meeting being held in Canada said communication of vital research on health and environment issues is being suppressed.
But one Canadian government department approached by the BBC said it held the communication of science as a priority.
Prof Thomas Pedersen, a senior scientist at the University of Victoria, said he believed there was a political motive in some cases.
"The Prime Minister (Stephen Harper) is keen to keep control of the message, I think to ensure that the government won't be embarrassed by scientific findings of its scientists that run counter to sound environmental stewardship," he said.
"I suspect the federal government would prefer that its scientists don't discuss research that points out just how serious the climate change challenge is."
The Canadian government recently withdrew from the Kyoto protocol to reduce carbon dioxide emissions.
The allegation of "muzzling" came up at a session of the AAAS meeting to discuss the impact of a media protocol introduced by the Conservative government shortly after it was elected in 2008.
The protocol requires that all interview requests for scientists employed by the government must first be cleared by officials. A decision as to whether to allow the interview can take several days, which can prevent government scientists commenting on breaking news stories.
Sources say that requests are often refused and when interviews are granted, government media relations officials can and do ask for written questions to be submitted in advance and elect to sit in on the interview.
Andrew Weaver, an environmental scientist at the University of Victoria in British Columbia, described the protocol as "Orwellian".
The protocol states: "Just as we have one department we should have one voice. Interviews sometimes present surprises to ministers and senior management. Media relations will work with staff on how best to deal with the call (an interview request from a journalist). This should include asking the programme expert to respond with approved lines."
Professor Weaver said that information is so tightly controlled that the public is "left in the dark".
"The only information they are given is that which the government wants, which will then allow a supporting of a particular agenda," he said.
The leak was obtained and reported three years ago by Margaret Munro, who is a science writer for Postmedia News, based in Vancouver. Speaking at the AAAS meeting, she said its effect was to suppress scientific debate on issues of public interest.
"The more controversial the story, the less likely you are to talk to the scientists. They (government media relations staff) just stonewall. If they don't like the question you don't get an answer."
Ms Munro cited several examples of what she described as the "muzzling" of scientists by the government.
The most notorious case is of that of Dr Kristi Miller, who is head of molecular genetics for the Department for Fisheries and Oceans. Dr Miller had been investigating why salmon populations in western Canada were declining.
The investigation, which was published in one of the leading scientific journals in the world, Science, seemed to suggest that fish might have been exposed to a virus associated with cancer.
The suggestion raised many questions, including whether the virus might have been imported by the local aquaculture industry.
The journal felt this to be an important study and put out a press release, which it sent out to thousands of journalists across the world. Dr Miller was named as the principal contact.
However, the government declined all requests to interview Dr Miller. It said it was because she was due to give evidence to a judicial inquiry on the issue of falling fish stocks.
According to Ms Munro, because reporters were denied the opportunity to question Dr Miller about her work, important public policy issues went unanswered.
"You have a government that is micromanaging the message, obsessively. The Privy Council Office (which works for the Prime Minister, Stephen Harper) seems to vet everything that goes out to the media," she said.
A spokeswoman for Fisheries and Oceans Canada told BBC News: "The Department works daily to ensure it provides the public with timely, accurate, objective and complete information about our policies, programmes, services and initiatives, in accordance with the Federal Government's Communications Policy.
"In 2011, Fisheries and Oceans publicly issued 286 science advisory reports documenting our research on Canada's fisheries; our scientists respond to approximately 380 science-based media calls every year."
Fisheries and Oceans Canada declined a request by the BBC to interview Kristi Miller for this article. Dr Miller told us she would have been willing to be interviewed had her department given her permission.
The AAAS meeting's discussion on muzzling is organised by freelance science reporter Binh An Vu Van. She says fellow journalists across Canada are finding it "harder and harder" to get access to government scientists.
Ms Vu Van claims that as well as "clear-cut cases of muzzling", such as the one involving Dr Miller, media relations officers use more subtle methods. She said that when she requests an interview, she has to enter into prolonged email correspondence to speak to a scientist she knows is ready and willing to be interviewed, often to be declined or offered another scientist she does not want to interview.
"It's so hard to get hold of scientists that a lot of my colleagues have given up," she explained.
Ms Munro cited another example of research published in another leading scientific journal, Nature, that was published last October.
An international team including several scientists from the government agency, Environment Canada, set out details of a hole that appeared in the ozone layer above the Arctic.
Ms Munro said she had called one of the scientists involved who she had dealt with several times in the past. He agreed to speak to her, but said that he had been told that her request had to be put to government media relations officials in Ottawa.
"So I phoned up Ottawa and they just said no you can't talk to the guy. A couple of weeks later, he was available but by then the story had been done. So they take them out of the news cycle," she said.
Ms Munro also claims that journalists were denied access to scientists working for the government agency Health Canada last year, when there was concern about radiation levels reaching the country's western coast from Japan following the explosion at the Fukushima nuclear power plant. Ultimately, journalists obtained the information they sought from European agencies.
The Postmedia News journalist obtained documents relating to interview requests using Canada's equivalent of the Freedom of Information Act. She said the documents show interview requests move up what she describes as an "increasingly thick layer of media managers, media strategists, deputy ministers, then go up to the Privy Council Office, which decides 'yes' or 'no'".
"The government has never explained what the process is. They just imposed these changes and they expected us to sit back and take it," she explained.
Professor Andrew Weaver believes that the media protocol is being used by the Canadian government to "instruct scientists to deliver a certain message, thereby taking the heat out of controversial topics".
He added: "You can't have an informed discussion if the science isn't allowed to be communicated. Public relations message number one is that you have to set the conversation. You don't want to have a conversation on someone else's terms. And this is now being applied to science on discussions about oil sands, climate and salmon."