Indonesia has said it is surprised, disappointed and deeply deplores the move, and labelled the group as economic migrants seeking a better life in Australia.
Jakarta has warned any decision to grant temporary visas to the group will affect diplomatic relations and open the floodgates for more Papuan refugee hopefuls.
On Thursday, Australian Immigration Minister Amanda Vanstone announced 42 of the 43 Papuans had received temporary protection visas and would be taken from Christmas Island to Melbourne.
In January, 36 adults and seven children from Papua landed on Cape York Peninsula in far north Queensland seeking asylum.
The asylum seekers claim that they would be killed if sent home, but Indonesian President Susilo Bambang Yudoyhono has denied the accusation and called on Australia to return them.
Ministers downplay situation
Immigration Minister Amanda Vanstone on Friday again rejected claims that granting protection visas to 42 West Papuans endorsed their claims of widespread human rights abuses by Indonesia.
She said the granting of the visas was a departmental decision, made after considering each person's individual circumstances.
Earlier Foreign Minister Alexander Downer said he hopeful that there would not be any diplomatic backlash from Indonesia over the decision.
"I hope not because bilateral cooperation is in our mutual interest, it's in Indonesia's interest as much as it's in Australia's interest," he told ABC radio.
He said Australia's position would not change even if there was diplomatic backlash from Jakarta.
"There's simply nothing we can do about it. We're just constrained by the laws of our land," Mr Downer said.
Jakarta statement
Jakarta said the decision would confirm in the minds of many Indonesians that many Australians supported separatists in the province of Papua.
"On numerous occasions, the Indonesian government at the highest level has made it absolutely clear that none of these self styled "asylum seekers" in question are being sought by the Indonesian authority for any reason whatsoever, nor are they being subjected to any persecution in Indonesia," the statement from the department of foreign affairs said.
The Indonesian government said that the grounds on which the Department of Immigration granted the visas were baseless and without legal merit.
"Indeed, the Indonesian government guaranteed their safety if they wish to return back to Indonesia,” the statement said.
Unfriendly act
It follows earlier verbal attacks from nationalist MPs in the Indonesian Parliament over the move.
Senior Indonesian nationalist MP Djoko Susilo said Australia's decision to grant the temporary visas was an unfriendly act that effectively challenges Indonesia's rule in Papua.
He added it would only incite the political situation in the province.
“We have to show our displeasure that what Mr Howard's government is doing is something contrary to the best interests of the Indonesian and Australian people,” Mr Susilo told SBS World News Australia.
Seeking asylum
The 43 Papuans risked a five-day voyage across the Torres Strait on a shanty outrigger before landing near the remote mining community of Weipa, in far north Queensland.
They displayed a large banner above the makeshift vessel that accused the Indonesian government of "genocide, intimidation and terrorist acts from the military”.
In 1969 a separatist movement was sparked after Jakarta moved to integrate Papua into Indonesia. Since then there has been a long-running campaign of unrest which recently has also triggered violence at a US-owned gold mine.
New hope: advocate
In the lead up to the decision, the asylum seekers had anticipated that the Australian Immigration Department would rule in their favour. After the announcement one of the West Papuans was optimistic for further developments.
"Yes, we feel good because we know that Australian have gave us and give [sic] the temporary visa, and we believe that they will also give us the permanent visa," said Henoch Frenghy Nawipa, one of the refugees.
A Papua-based human rights advocate said that the move has increased hope within the community there, that Australia could be more open to discuss the human rights problems of the province with the Indonesian government.
“I think what they are saying is that in terms of human rights issue [sic] the Australian government is somehow on the side of people who have been struggling to defend their rights,” Dr Benny Giay told SBS in a phone interview speaking from Elsham Jayapura.