Foreign Affairs Minister Julie Bishop has revealed it was not the Australian spy chief's idea to pose for a controversial photo with Philippines President Rodrigo Duterte.

Key points: A photo shows both Duterte and Warner in the President's trademark fist-pumping pose

A photo shows both Duterte and Warner in the President's trademark fist-pumping pose Bishop says she is "confident" the photo was not Mr Warner's idea

Bishop says she is "confident" the photo was not Mr Warner's idea Human Rights Watch says the image suggests "tacit support" for extrajudicial killings in the Philippines

ASIS director-general Nick Warner met Mr Duterte at the presidential palace in Manila on Tuesday.

In a photo taken by the President's staff, both are seen with their right hands in a fist — Mr Duterte's trademark fist-pumping pose.

"I understand that the action — the fist pump — was not the director-general's idea. He was responding to a request from the President of the Philippines," Ms Bishop said.

She pointed out Mr Warner had been a guest of the President and said she was "confident" the photo was not Mr Warner's idea.

Ms Bishop made it clear she would prefer the spy chief's activities stayed secret.

"Of course Australia's secret intelligence service is called our secret intelligence service for a reason, so preferably the work that ASIS does is below the surface, but there are instances where it becomes public," she said.

After assuming power last June, Mr Durtete's drug crackdown has seen thousands of extrajudicial killings across the South-East Asian nation.

Human Rights Watch Australia director Elaine Pearson has criticised Mr Warner's photo with Mr Duterte.

"I think a picture like this really does tend to sort of suggest Australia's tacit support for these killings," she said.

"You wouldn't pose for a photo like that with a mass murderer, and one day we certainly hope that Duterte may eventually be indicted for crimes against humanity."

Ms Pearson said Mr Warner and the Australian Government needed to clarify their positions on Mr Duterte's war on drugs.

Fears photo will be used for 'propaganda purposes'

Labor's Anthony Byrne, deputy chairman of Parliament's intelligence and security committee, has rarely — if ever — publicly criticised Australia's spy agencies.

But he said the photo was completely inappropriate.

Mr Byrne told the ABC he had taken a number of phone calls from members of the intelligence community who expressed concern about the photo.

"They have described it as a serious misjudgement which will undoubtedly be used for propaganda purposes," he said.

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But the head of the Strategic and Defence Studies Centre at the Australian National University, John Blaxland, urged people to cut Mr Warner some slack.

"Nick Warner is really going the extra mile here trying to fit in, trying to accommodate Duterte's idiosyncrasies," Professor Blaxland said.

"Anybody can take a photo in a spilt second and capture people doing something that appears odd.

"He was representing Australia, he was doing his bit, he's trying to work on the relationship with President Duterte."

Mr Warner is a former Defence Department secretary and long-serving Department of Foreign Affairs and Trade official.

A presidential spokesman told local media the spy chief visited to affirm "mutual support".

The Philippines has been waging a furious campaign against Islamist militants in the city of Marawi.

Australia is increasingly worried about the flow of foreign fighters back into South-East Asia from conflicts in the Middle East.