An asylum-seeker swap deal with Malaysia is expected to be finalized in the coming weeks while Jakarta discarded a similar deal with Indonesia by the federal government.

Immigration Minister Chris Bowen expressed his satisfaction with the development of the negotiations between Canberra and Kuala Lumpur regarding a deal which will allow Australia to swap 800 asylum seekers for 4000 people with refugee status from Malaysia.

Australia’s recent deal with Malaysia aimed to include the asylum-seekers who arrived by boat even before the agreement was finalized. Moreover, the government was eager to pursue similar deals with other nations in the region.

On the other hand, Indonesian Foreign Minister Marty Natalegawa rejected the possibility of his country entering into a swap agreement with Australia as he intends to focus on expanding a regional framework.

"What Indonesia has been doing with Australia is to develop the regional architecture ... so we have not been contemplating a bilateral approach," Marty said after a meeting with foreign ministers.

Knowledgeable of the deal between Australia and Malaysia, Natalegawa described it to be countering wider regional efforts aimed at combating people smuggling and stopping the flow of asylum-seeker boats.

Details of Bowen’s discussions with United Nation’s human rights Chief Navi Pillay will not be revealed as Pillay warns that the swap deal may be illegal because of the affairs on Malaysia’s human rights record.

"She did very much welcome the conversation that we had and told me that she was warmed by some of things that I explained to her," Bowen said.

Australian Greens senator Sarah Hanson-Young said time is the greatest factor that can deter asylum seekers from making the boat journey to Australia. "We know from history that when people are in a very desperate situation, they take whatever means necessary," she said.

Since the deal was first flagged Christmas Island served as a legal limbo for at least 107 people – seventeen of them are children as young as young while nine are unaccompanied minors – floating in the waters of the Western Australian coast, added Hanson-Young.

According to Senator Hanson-Young, "Immigration Minister Chris Bowen is undermining his role as guardian to protect these kids simply to uphold what is a poorly patched together agreement with a country which has not signed the refugee convention."