The Prime Minister has refused to comment on reports that Australian spies gathered intelligence for the United States on Indonesian trade negotiations last year.

The New York Times has reported that a document obtained by former National Security Agency (NSA) contractor Edward Snowden shows the Australian Signals Directorate carried out surveillance on a US law firm representing Indonesia.

Mr Abbott says he never comments on operational intelligence matters, but says anything that is gathered is not used to the detriment of other countries.

"We use it for the benefit of our friends," he said.

"We use it to uphold our values. We use it to protect our citizens and the citizens of other countries and we certainly don't use it for commercial purposes."

Relations between Australia and Indonesia plunged to their lowest ebb in years in November after reports that Australia tried to tap the phones of president Susilo Bambang Yudhoyono, his wife and several top officials in 2009.

Jakarta responded furiously to the claims, which were based on documents leaked by Snowden, recalling its ambassador and suspending cooperation with Australia on key areas including people smuggling.

Fresh claims published in the New York Times on Sunday alleged Australian agencies spied on Indonesian officials during a trade dispute with the US and offered to share back-room information with the NSA.

The top secret 2013 document allegedly obtained by the Times did not say which trade dispute was monitored nor name the US law firm involved.

Indonesia has been embroiled in trade disputes with the US over its exports of clove cigarettes and shrimp in recent years.

The latest leak comes as US secretary of state John Kerry visits Indonesia and as tensions simmer between Canberra and Jakarta over Operation Sovereign Borders.

Indonesia's foreign minister Marty Natalegawa has said he would raise Australia's asylum seeker policies with Mr Kerry, describing them as "against the values of humanity".

Australian warships have strayed into Indonesian waters during border patrol operations, although Canberra insists the intrusion was inadvertent.

Mr Abbott said Australia "deeply respects Indonesia's sovereignty".

"We want to work as close as possible with Indonesia to crack down on the scourge of people smuggling, which as we all know has cost this country dear," he said.

The Federal Government has blasted Snowden, with Foreign Minister Julie Bishop lashing out at his "unprecedented treachery" and describing him as "no hero" in a speech in Washington last month.

ABC/AFP