The ABC has also stepped up pressure on the Coalition, writing to Home Affairs Minister Peter Dutton demanding an immediate end to police action against two senior reporters following a raid on the ABC's Sydney headquarters last month.

"We cannot fulfil our legislative remit if our journalists are intimidated or treated like criminals," the broadcaster's managing director, David Anderson, told staff on Thursday.

In an interview with The Sydney Morning Herald and The Age, human rights commissioner Edward Santow said the recent police raids on ABC and News Corp journalists would be "unthinkable" in the United States and United Kingdom. But he praised Prime Minister Scott Morrison for acting quickly by ordering an inquiry into the clash between national security and the public's right to know.

"I think the raids have really shone a light for the entire Australian community that we need to have targeted laws that protect us against serious crime but that don't go any further than absolutely necessary in impinging on basic rights, and those rights include media freedom," Mr Santow said.

"We accept it's necessary to have laws that may impinge to some extent on rights like privacy in order to protect the community against serious crimes. But our fundamental concern is that the law goes further than it should and breaches a number of human rights."

Federal MPs are conducting a major review of the Abbott-era mandatory data retention regime, which forces telcos to store their customer's detailed phone and internet records for two years.

The system also allows police to access the metadata of journalists in a bid to identify sources, provided investigators apply for a warrant. The Australian Federal Police (AFP) used the laws to access journalist metadata 58 times in just one year.

Mr Santow said the mandatory two-year retention period was a "blunt instrument" and storing the private information of Australians "just in case it might be useful at some hypothetical later date" was unacceptable.

He did not nominate a preferred new retention period but noted court verdicts in Europe sought to limit data retention to no more than three or six months.

Between 2015 and 2018, the AFP accessed metadata less that was less than three months old on about 40,000 occasions. Metadata between one and two years old was accessed just 3163 times.

The biggest change proposed by the Australian Human Rights Commission is a new requirement for police to obtain a warrant before they access anyone's metadata - a recommendation that will be strongly opposed by law enforcement agencies because it would slow down the investigation process.

"We say it's worth the effort because people's basic rights are at issue," Mr Santow said. "But we have also seen that a warrant may make it less likely that there will be overuse of accessing metadata."

While police are overwhelmingly accessing metadata for serious criminal investigations - particularly terrorism and drug offences - they are also using it to probe more minor things like traffic infringements.

Mr Santow called for a comprehensive review of Australia's legal and privacy system because the rapid development of communications technology would inevitably lead to even more government legislation.

"Since 2001, we have passed literally dozens of laws that basically enable a range of ways for the government to access our personal information and over 18 years those laws add up," he said.

"What we have never done in Australia in that time is to take a step back and have a comprehensive review of the inter-relationship of those laws and whether all those laws go absolutely further than they need to in impacting on our basic human rights."

The AFP has argued no changes are needed to the overall metadata regime.

"Access to telecommunications data is a critical investigative and intelligence gathering tool. It is used in almost all investigations into criminal activity, serious civil infringements and of intelligence matters," a spokeswoman said.

A separate parliamentary inquiry into press freedom is also slated to begin soon and report by mid-October.

The ABC's letter to Mr Dutton was sent after The Sydney Morning Herald and The Age revealed the AFP asked Qantas to hand over the private travel records of a reporter as part of its controversial investigation into a major national security leak.

An AFP statement shows investigators approached Qantas earlier this year asking for information about Daniel Oakes, one of two ABC reporters who broke the story known as "The Afghan Files".

The document is dated April 1 this year and headlined "Statement in the matter of R v Daniel Michael Oakes", suggesting police could be building a case against the reporter in addition to pursuing the Defence whistleblower who has already admitted to leaking the information.

"As we have seen in media reports this week, the ability of law enforcement and security agencies to secretly monitor the activities of journalists is deeply concerning," the ABC's managing director told staff on Thursday.