Jakarta – Indonesia has recalled its ambassador to Australia amid a furore over Canberra's decision to grant temporary visas to 42 asylum seekers from restive Papua province.

Indonesian foreign ministry spokesman Yuri Thamrin said its envoy would be called back to Jakarta for "consultations" with foreign ministry officials over the matter.

"It is not a permanent recall, but it is important because there are issues that need to be discussed over this incident," Thamrin told a press briefing.

He said Indonesia would not overreact but its response "will be calibrated and this type of response we believe is suitable." Australia said this week it had granted visas to all but one of the 43 Papuans who arrived in the north of the country by boat in January.

The Papuans, who include pro-independence activists and their families, have accused Jakarta of "genocide" in troubled Papua, a former Dutch colony taken by Indonesia in the 1960s.

Indonesian Foreign Minister Hassan Wirayuda told reporters that the recall would take place "as soon as there's a flight that can take our ambassador home," the Detikcom online news agency reported.

Australia's envoy in Jakarta, Bill Farmer, was also summoned to the foreign ministry Thursday and told of Indonesia's "disappointment and our dismay," Thamrin told AFP earlier.

Speaking ahead of the recall, Australia's Foreign Minister Alexander Downer said while he expected "protests of one kind or another from Indonesia" over the decision he did not think it would affect bilateral relations.

"I think they'll be some protests from Indonesia but I think things will settle down after a short period of time," he told reporters.

Indonesia released a statement late Thursday saying the government was "surprised, disappointed and deeply deploring" of Australia's decision to grant the visas.

It said Jakarta had made "absolutely clear" that none of the Papuans were being sought by the authorities and were not subject to any persecution.

"Indeed, the Indonesian government guaranteed their safety if they wish to return back to Indonesia. The decision (to grant the visas)... is therefore baseless and without any legal merit," the statement added.

Indonesia also said Australia's action "justifies speculation" that elements there supported separatist movements in Papua which Canberra had failed to act against.

Australia also insisted Friday that it remained opposed to independence for Papua where a separatist movement has simmered since it came under Jakarta's rule.

Downer, who personally informed his Indonesian counterpart Wirajuda of the decision by telephone, also said that the visas were issued in Australia following legal procedures.

"This isn't a decision that's made by the Australian government, but through a process which is set in Australian law... we're certainly not in any way changing our position on the recognition of West Papua as part of the Republic of Indonesia," he told Australian radio. "We retain that view very strongly, that West Papua must remain as part of Indonesia."

The sometimes difficult relations between Jakarta and Canberra Jhad been steadily improving under President Susilo Bambang Yudhoyono, Indonesia's first directly-elected president.

Bilateral ties hit a low point in 1999 when Australia led peacekeeping troops into the then-Indonesian province of East Timor to halt violence by pro-Jakarta militia following the territory's vote for independence.