Tony Abbott has signalled he is unlikely to agree to allow journalists to contest applications to access their call logs and other metadata.

The prime minister and the opposition leader, Bill Shorten, have been negotiating on the form of words for an amendment requiring agencies to seek a court warrant if they wish to obtain journalists’ metadata for the purpose of determining sources.

Abbott agreed on Monday to make such an amendment to his proposed data retention laws, but media industry representatives want the warrant application process to be “contestable” so journalists’ lawyers could argue their case for protecting confidential sources.

It is understood media representatives are growing increasingly frustrated at their exclusion from the negotiations between the Coalition and Labor over the shape of the amendment.

A major point of contention is the threshold test for judges to grant a warrant.

Media representatives want the amendment to enshrine a presumption in favour of press freedom, and a requirement for agencies seeking metadata to prove that the principle was outweighed by the legitimate reason for access.

This would be similar to the arrangements contained in the federal shield law, which notes “the public interest in the communication of facts and opinion to the public by the news media and, accordingly also, in the ability of the news media to access sources of facts”.

Abbott declined on Wednesday to “give a running commentary on what are constructive and collegial discussions between the government and the opposition”.

But he gave a strong signal that the government would not agree to a contestable process.

“What we are proposing is a level of protection for journalists’ metadata which simply doesn’t exist now,” he said.

“There is no special protection for journalists’ metadata right now, so we are proposing much greater protection for journalists’ metadata than is currently the case, than has ever been the case, but I think there’s a misunderstanding about the warrant process.

“I’ve never practised as a lawyer but my understanding is that where the police or security agencies want a warrant, they go before the relevant judicial officer, they make a case, the officer considers the case and says yes or no to the activity for which a warrant is proposed.

“These things are never contested. A contested warrant is more like a court case and if you had to have a court case to access metadata, well, the whole process would absolutely gum up.”

When asked to reflect on whether he would have been comfortable with an uncontested process when he was a journalist, Abbott repeated his general point that existing laws allowed agencies to access metadata without a warrant.

“In the days when I was a journalist [the 1980s] there were no metadata protections for journalists and if any agency including the RSPCA or the local council had wanted my metadata they could have just got it on authorisations, so, look, I was perfectly comfortable as a journalist,” he said.

Abbott said he believed that Australian police and security agencies operated “in a fair and reasonable and responsible manner”.

The Australian federal police (AFP) confirmed on Tuesday that it had sought journalists’ metadata under existing warrantless access arrangements, but said this was only in “rare” cases.

The commissioner, Andrew Colvin, said in the past 18 months the AFP had received 13 referrals relating to the alleged unauthorised disclosure of commonwealth information in breach of section 70 of the Crimes Act.

“In the overwhelming majority of these investigations, no need was identified to conduct a metadata telecommunications inquiry on a journalist,” Colvin said. “AFP requests for accessing a journalist’s metadata are rare.”

The government has set a deadline of next week for parliament to pass data retention laws requiring telcos and internet service providers to store customers’ details for two years.

The lower house continues to debate the bill, but the amendment relating to journalists is yet to be proposed in the chamber.