The Australian Embassy's coat of arms in Jakarta has been defaced with paint and abusive graffiti during rallies against the Federal Government's decision to grant 42 Papuans visas.

Protests over the visas were reported in three Indonesian cities on Monday, including two separate rallies involving several hundred chanting protesters who targeted the Australian embassy in Jakarta.

Protesters waved placards with slogans including "Go to hell Australia, the devil needs you there!"

The protesters also threw paint at the embassy's coat of arms and scrawled graffiti saying "Get out of Indonesia immediately" and "Australia f......."

"Don't turn Papua into a second East Timor," one of the demonstrators was broadcast as saying on ElShinta radio, referring to the former Indonesian territory that became an independent nation in 2002.

The visa incident is the worst to hit relations since 1999 when Australia led peacekeeping troops into East Timor, then an Indonesian province, to halt violence by pro-Jakarta militias following the territory's vote for independence.

The Indonesian Government has been criticised by The Jakarta Post over the row with Australia.

"Instead of calming the situation, Jakarta has aggravated it. A diplomatic spat turned into a political crisis between two nations who really have nothing to quarrel about," the paper says.

"The allegations of abuse made by our Papuan brothers seeking asylum may, as the government claims, be utterly false. But by reacting in such a way, Indonesia is actually raising suspicion ... that something is amiss in Papua," the paper says.

"This spat must be resolved now. Delay only augments acrimony amidst a hungry public eager to blame someone."

The criticism followed efforts by Australia's envoy to Jakarta to reassure the government that Australia wants Papua to remain a part of Indonesia as he sought to allay anger over the visas.

Ambassador Bill Farmer's attempt to smooth over the worst incident between the neighbours since 1999 came as Indonesia postponed signing an agreement on Australian assistance to fight bird flu with $10 million of funding.

"This postponement is linked to the granting of the visas," Lalu Mara Satria Wangsa, from the welfare minister's office, told AFP.

"The Government has one voice on this," he said, adding that the agreement would be signed when "diplomatic relations are more conducive" to it.

Mr Farmer told reporters that Australia wholeheartedly backed Indonesian rule over Papua, echoing Prime Minister John Howard's conciliatory words over the weekend.

"The Australian Prime Minister, our foreign minister and the Australian Government have made it very clear in recent days that Australia recognises Papua as an integral part of Indonesia and we do not support, and will not support, separatism in Indonesia," Mr Farmer said.

Speaking after talks with Defence Minister Yuwono Sudarsono, Mr Farmer repeated that "the Government's position is that Australia unreservedly and strongly recognises Papua as part of Indonesia".

His statement came amid mounting anger after temporary visas were granted to all but one of 43 Papuans who landed in Australia in January seeking asylum, citing persecution and genocide by the Indonesian military in Papua.

The province has been the scene of a low-level separatist revolt since Indonesia took it over from Dutch colonisers in the 1960s.

Rights groups have accused security forces of abuses there.

Indonesia recalled its ambassador last Friday to signal its anger.