Email correspondence between 470 fellows at the Australian Academy of Science, obtained by Fairfax Media, reveals some of the nation's leading researchers are intimidated by the law and fear it will have a chilling impact on academic freedom.

The laws, which came quietly into effect on Saturday night, require Australian scientists working on projects of interest to military or intelligence services to seek permission before consulting overseas colleagues.

Those who discuss their work without permission risk fines or possible jail time. The laws provide the government with visibility and control over sensitive material that may pose a risk to national security.

Melbourne-based Professor Laureate Peter Doherty, an immunologist who won the Nobel Prize for physiology or medicine in 1996, told his colleagues the law would intimidate scientists and be ineffective, given "neither nature nor bad guys obey any such rules".

Professor Laureate Jon Borwein, a fellow at the Australian Academy of Science and mathematician at the University of Newcastle, told Fairfax Media he feared his interaction with Israeli and Iranian assistants would make him a suspect.

"This extra level of uncertainty is chilling enough to have me say 'no' when before I might have said 'tell me more' when I get a request for a visit of information," he said.

The two scientists are at odds with the academy, which supported the amendments to the Defence Trade Controls Act that granted defence veto powers, effective from Saturday.

The academy is a routine recipient of government funding, including a $178,000 payment from the Department of Defence for scientific study services in early 2014.

According to the bill's explanatory memorandum, Australia's university sector relies heavily on international collaboration and routinely supplies sensitive controlled information.

"Leaving this activity unregulated would undermine Australia's international reputation as a credible contributor to global counter-proliferation efforts," the bill said.

Those working on sensitive projects involving electronics, computers, information security, aerospace, telecommunications and nuclear materials are likely to have their work closely monitored by the Department of Defence.

Professor Les Field, secretary of policy at the academy, said he did not believe the law was designed to deliberately intimidate scientists.

"We have yet to be alerted to any cases where scientists have been advised by Defence that they are unable to continue their international collaborations, and the actual impact of the act so far appears to be relatively low," he said.

"However, we have heard from a number of scientists who are confused about the Act and whether it applies to them."

Associate Professor Gilda Tachedjian, a scientist with the Burnet Institute, said the law would "have serious consequences on Australia's competitiveness in medical research and stymie the Turnbull Innovation agenda".

Professor Tachedjian is one of hundreds of scientists who have signed a petition calling on Prime Minister Malcolm Turnbull to make research and public education exempt from the law.

Associate Professor Michael Lardelli, a scientist at The University of Adelaide, signed the petition and described the law as counter-productive and based on fear.

"Don't broadly stifle innovation on the grounds of obscure fears of exporting technologies that might, one day, be incorporated by the military forces of other nations," he said.

Dr Ian Ross, a senior biologist at the University of Queensland also signed the petition, fearing his work would be at risk of inadvertently breaching the law.

"This will have a chilling impact on Australian science," he said.

Most universities in Australia have warned academics of the risk they face in researching certain topics without a permit, although the National Tertiary Education Union has warned the liability for criminal activity rests with the researcher.

Civil Liberties Australia chief executive Bill Rowlings said the requirement was a militarisation of the research that curtailed liberties, rights and freedoms.

"They can speak about their work internationally … but only if and when and how and where the Australian Defence Department approves," he said.

Daniel Mathews, a lecturer in mathematics at Monash University, said the law was undoubtedly a case of government overreach and would impact many of his colleagues working in computer science and chemistry.

"They face a difficult choice: apply for a permit every time they start a new project, with all the associated delays and red tape, or hope the law wouldn't cover them despite the uncertainty, and carry on as before," he said.

The Department of Defence was contacted for this story.