More than 330 asylum seekers who were to have been sent to Malaysia will now be processed on Christmas Island as Federal Cabinet meets today to discuss the matter.
The asylum seekers have been in limbo since the High Court scuttled the government's deal to send 800 boat people to Malaysia.
Mr Bowen said it was now necessary to process their refugee claims on Christmas Island.
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"Every processing takes time as their claims are assessed, but their processing will commence," he told ABC Radio.
If they were found to be genuine refugees, they would be settled in Australia, he said.
The government is considering all its options regarding asylum seekers, including the possibility of changing the Migration Act to allow offshore processing in Nauru and Papua New Guinea, Mr Bowen said.
Opposition Leader Tony Abbott has offered to help pass any such legislation.
Cabinet will meet on Monday to discuss the matter.
Mr Bowen said offshore processing was "not a silver bullet" to stopping boat arrivals.
"I think that Nauru and PNG when they were in the (Howard government's) Pacific Solution were ... a game of bluff," he said.
"I think there were a range of factors which led to the slowing of the boats ... the fall of the Taliban in Afghanistan, the peace accord in Sri Lanka.
"The ultimate deterrent is to say if you get on a boat and come to Australia you'll be returned."
SUPPORT DROPS FOR ASYLUM POLICY
Support for the federal government's management of asylum seekers has collapsed, a new poll shows.
A Newspoll published in The Australian on Monday found 78 per cent of respondents rated Labor's handling of the issue as "bad".
This is an increase on the 53 per cent recorded by Newspoll in November 2009.
The poll was conducted over the weekend in the wake of the High Court ruling that scuttled Labor's Malaysian people swap deal.
Just 12 per cent of voters rated Labor as the best party to handle asylum seekers, compared to 38 per cent for the coalition.
The full Newspoll will be published on Tuesday.
LABOR MUST COME UP WITH A PLAN: ABBOTT
Opposition Leader Tony Abbott says it's up to the Gillard government to work out exactly how to change the law to put offshore processing of asylum seekers beyond legal doubt.
Mr Abbott has offered to help Labor change the Migration Act to provide legal certainty following last week's High Court ruling which sank Julia Gillard's Malaysia deal.
But he says it's not up to the opposition to provide the detail.
"We can't save the country from opposition," Mr Abbott told reporters in Canberra.
"It's really up to the government to come to us with a proposal."
The opposition leader said he wanted to be constructive and help the government "put beyond legal doubt offshore third-country processing".
Asked whether the offer of assistance extended to allowing processing in Malaysia, Mr Abbott said the deal with Kuala Lumpur was always a bad one.
"But I'm not in the business of ruling things in or ruling things out."
Pressed on whether the Act could be changed to be "Nauru-specific", Mr Abbott said he didn't want to be "too prescriptive here".
"I am trying to make it easier for the prime minister to go down the path of third country processing," he said.
Mr Abbott said the ball was in the prime minister's court and he hoped she'd return it.
He said he did not want to give Ms Gillard "any excuse" to cave into the Greens or the left of the Labor party that would completely abandon offshore processing.
He was not asking the government to embrace the entirety of the coalition's policy that included temporary protection visas, but he was prepared to work constructively with the government to put offshore processing beyond legal doubt.
"This is my attempt to be as constructive as I possibly can be in the very difficult circumstances that the government finds itself in, and frankly, the difficult circumstances that our country finds itself in," Mr Abbott said.
"We now have a government with no border protection policy whatsoever. I'm giving them the option of resurrecting elements of their former policy, and I think they should take it."
