The laws require Australian scientists researching projects of interest to military or intelligence services to seek permission from the government before consulting with overseas colleagues.

Those who discuss their work without permission risk fines or possible jail time.

The amendments, which came into effect on Saturday after a 12-month grace period, provide the government with visibility and control over sensitive material that may pose a risk to national security.

"Australia's relatively small university and research sector relies heavily on international research collaborations and will supply sensitive controlled technology in the course of that collaboration," the bill's explanatory memorandum said.

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

The monitoring regime, implemented by the Defence Export Control Office, requires academics working on research dubbed "controlled activity" to apply for in principle approval before exporting their work.

It applies to those working in electronics, computers, information security, aerospace, telecommunications and nuclear materials.

When first proposed, the National Tertiary Education Union criticised the amendments as unacceptable government oversight.

"The assignment of a prohibition power to the Defence Minister has new and unrivalled implications for the freedom of expression of a professional group that fundamentally depends upon the capacity to communicate and share findings," NTEU national president Jeannie Rea said.

"There are criteria within the proposed regulations that allow for the defence minister to make prohibitions or deny a permit for supply of dual use technologies that are an overreach of the obligations defined through existing treaty instruments.

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.

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

"Traditionally, scientists and researchers have enjoyed the civil liberties of being able to exchange information subject only to their common sense in not imparting secrets internationally that should not be shared," he said.

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

Dr Mathews said there were a number of exemptions in the law although  they were uncertain and provided no comfort to innovators in academia or industry.

"In particular there is no exemption for activity in the ordinary course of scientific research," he said.

"The result is major legal uncertainty and risks for anyone involved in any of the prescribed areas – which will filter through risk-averse university bureaucracies."

According to the NTEU, some universities have already misinterpreted the legislation to impose unnecessary administrative burden on academic staff. The union has also warned members criminal liability falls upon individuals rather than universities.