THE Australian flag has been burned by protesters in Indonesia and hundreds of riot police are on standby in Jakarta amid the ongoing fallout over the government spying controversy.

Officers have been stationed at the Australian embassy in Jakarta in preparation for protests over the tapping of Indonesian President Susilo Bambang Yudhoyono's phone.

More than 100 of the Indonesian National Police's Mobile Brigade (BRIMOB), armed with riot shields and tear gas, were called to the embassy on Thursday.

Another 300 BRIMOB officers were on standby at a nearby location, a police spokesman told AAP.

There were also balaclava-clad security officers with binoculars stationed on an overpass close to the compound.

Demonstrators in the Indonesian city of Yogyakarta have already burnt an Australian flag in protest over the alleged tapping as anti-Australian sentiment continues to escalate.

The large group of protesters in Yogyakarta, a hotbed of student activism, had demanded an apology from Prime Minister Tony Abbott and asked the Indonesian president to sever diplomatic ties with Canberra, reports said.

Mr Abbott addressed parliament on the controversy today, confirming he has received a letter from the Indonesian President sent in the wake of the suspension of militarily and asylum seeker cooperation.

"I want to assure the House that the government will respond swiftly, fully and courteously to the President," Mr Abbott said.

"As always, my intention is to do everything I reasonable can to strengthen this relationship which is so important to both our countries."

Opposition Leader Bill Shorten pledged bipartisan support to the government.

It's understood the government has already undertaken precautions to ensure the safety of staff at the embassy in Jakarta before today's protest.

The Department of Foreign Affairs and Trade (DFAT) has updated its travel advice in response to the protest plan.

"Local police advise that a demonstration is planned for outside the Australian Embassy,'' DFAT said.

"Australians should monitor local media, avoid protests, maintain high levels of vigilance and security awareness.''

The ramping up in nationalism and anger towards Australia came as a close confidant of Dr Yudhoyono warned relations with Australia may not recover unless Mr Abbott apologised over the spying allegations that prompted the current diplomatic crisis.

Ramadhan Pohan, whose niece is married to the president's oldest son, has urged Mr Abbott to apologise over the spying row by Thursday night.

Mr Ramadhan is also an MP with Dr Yudhoyono's ruling Democrat Party and a member of the parliament's powerful foreign affairs and defence committee.

``If Abbott does not apologise by (Thursday) night ... I predict that it will be the last night of Indonesia and Australia's friendship,'' Mr Ramadhan reportedly told Metrotvnews.com late on Wednesday night.

The warning came in the wake of Dr Yudhoyono's announcement on Wednesday that Indonesia was immediately cutting defence ties and co-operation on efforts aimed at combating people smuggling.

Dr Yudhoyono said he would send a letter to Mr Abbott, demanding an official apology and a full explanation as to why Australian spies targeted his mobile phone in 2009, as well as his wife's and some of his closest confidants.

Dr Yudhoyono said he wanted a personal explanation, insisting comments directed at ``Australia's domestic community'' would not suffice.

Australia's Defence Signals Directorate targeted President Yudhoyono's phone and that of his wife and senior officials in 2009, weeks after three Australians were killed in terrorist bombings in Jakarta.

At a joint press conference in Washington, US Secretary of State John Kerry and Australian Foreign Minister Julie Bishop refused to be drawn on the spying scandal.

Mr Kerry, speaking at the end of AUSMIN talks in Washington, refused to buy into the diplomatic row between Australia and Indonesia over spying claims.

"We just don't talk about intelligence matters in public and we're not going to begin now,'' he told reporters when asked whether the US had asked Australia to tap the phones of President Susilo Bambang Yudhoyono and his inner circle.

Australia monitors civil and military communications in Asia as part of its role in the "Five Eyes'' signals intelligence alliance that also includes the United States, Canada, the UK and New Zealand.

Washington also announced that President Barack Obama will visit Asia in April to push closer ties.

Susan Rice, Obama's adviser for national security, acknowledged disappointment after Obama called off a trip in October - which would have included Indonesia - to negotiate with Republican lawmakers who shut down the US government to stop his health care reforms.

Rice said Obama would make up with a trip in April.

"Our friends in Asia deserve and will continue to get our highest-level attention," she said.

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