Tony Abbott has accused Australia's national broadcaster of acting as an "advertising amplifier for the Guardian" by collaborating on the story that revealed intelligence agencies' attempts to tap the Indonesian president's phone.

The prime minister levelled the criticism at the ABC during an interview with the conservative commentator Andrew Bolt on Sunday, while conceding of that revelation that "plainly it was a story".

Guardian Australia and the ABC jointly revealed on 18 November that Australian spies attempted to listen in on the personal phone calls of the Indonesian president, Susilo Bambang Yudhoyono, and targeted the mobile phones of his wife, senior ministers and confidants.

The story was based on a top-secret document, dated November 2009, supplied by the former US intelligence contractor Edward Snowden. It led to a diplomatic stand-off between Australia and Indonesia, with Yudhoyono demanding a full explanation and then calling for a code of ethics between the two countries surrounding intelligence matters in future.

The ABC's managing director, Mark Scott, told a Senate estimates hearing that Guardian Australia approached the ABC about working in partnership on the story, similar to the Guardian's collaboration with other major publishers over previous leaked documents.

Abbott indicated he would have had no problem with the ABC reporting the story once the Guardian had published but questioned the partnership, which led to a synchronised release. Both media outlets mentioned the collaboration with the other when covering the issue.

"I think it's fair enough for people to question the judgment of the ABC, not in failing to cover the story as it were, because plainly it was a story, but in choosing to act as, if you like, an advertising amplifier for the Guardian," Abbott said on Ten's Bolt Report.

"It was the Guardian's story which the ABC seemed to want to advertise, even though there's not normally advertising on the ABC."

Asked if he would have liked more of the documents to be censored, Abbott said it was up to news organisations to consider what was fit for publication and broadcast.

"They have to make their own judgments but I think people are entitled sometimes to question the judgments news organisations make," Abbott said.

During the interview Bolt told Abbott the ABC was "out of control" and needed a new charter to deliver "some balance". Abbott resisted the call, saying he was "not in the business of making unnecessary enemies" or further inflaming critics.

Although the prime minister sometimes questioned the judgments of individual journalists, programmes and news organisations, he said he was "not in the business of putting anyone into particular camps because my job is to try to be appealing as I can at all times".

Abbott declined to say whether Australia privately assured Indonesia it would not conduct such high-level spying in the future, saying only that he wanted to increase intelligence sharing between the two countries.

"There've been all sorts of conversations at all sorts of levels between Australian and Indonesia over the last week or so and the point that all of us have made, from me down, is that we won't do things to hurt Indonesia, we will do things to help Indonesia."

Abbott said Yudhoyono's response was "very warm and friendly" as both leaders wanted the relationship between the two countries to be as strong as possible. Abbott's initial action after the story was published was to tell parliament that he would not apologise for the spying. Indonesia threatened to stop co-operation on issues such as people smuggling and is now demanding a code of ethics between the two countries.

"I was always happy to speak with the president but I thought it was important for him to digest all the various news reports and do what he thought was best, take what action he thought appropriate, and then of course we responded," Abbott said.

The interview is the second Abbott has granted Bolt since the September election. In the last encounter, published in News Corp publications in October, Abbott described as "complete hogwash" attempts to link the New South Wales bushfires to climate change. That interview also focused on the ABC's conduct.

At a Senate hearing on 19 November Scott argued the spying disclosures were in the public interest, as they raised questions about the nature and extent of intelligence gathering in the digital age, how information was shared and the security of that information.

Scott said parts of the documents were redacted based on advice from Australian authorities and he dismissed any suggestion the release was timed to damage Abbott's political standing. Scott told the hearing Snowden had released a massive volume of documents to the Guardian and it took time to examine all the material. He said he understood Guardian Australia had received the Indonesia spying documents only a short time before publication.

"The Guardian came to us," Scott said. "We worked in partnership with them. We did investigate the story independently and report the story independently." He suggested the ABC was able to offer Guardian Australia reporting depth and a broadcast platform.