Yesterday Rudd telephoned the Indonesian president.
Susilo Bambang Yudhoyono told him that people smuggling isn't just one country's problem.Defence Minister Stephen Smith is expected to meet with his Indonesian counterpart in Perth later today.
Indonesia correspondent George Roberts reports.
GEORGE ROBERTS: It's the evening call to prayer in Cisarua south of Jakarta where an Afghan called Muhammad Juma and his fellow asylum seekers are contemplating what to do now.
MUHAMMAD JUMA (translated): Right now we don't have any choice. What should we do? All the people wanted to go by boat. I went by boat, the boat broke and I was rescued but the others have gone again.
GEORGE ROBERTS: Australia's deal with Papua New Guinea is aimed at stopping thousands of asylum seekers like Muhammad Juma from leaving Indonesia.
Tantowi Yahya is a member of Indonesia's Foreign Affairs Commission. He says most of the 35 members are unhappy about not being informed of the deal.
TANTOWI YAHYA: The first thing that your country or the Prime Minister should contact is the minister of foreign affairs because he's dealing with this. And I've spoken with the minister a day after the announcement, he said he doesn't know anything about it.
GEORGE ROBERTS: The foreign minister Marty Natelegawa has refused to comment on the PNG arrangement. In the past he's said that Indonesia wouldn't support policies that put the burden back on Indonesia.
Mr Tantowi says the PNG deal does just that.
TANTOWI YAHYA: Now the terms of burden sharing I think should be applied in the real, in the real way. It's not only something that we speak about but really have to do that. It's a burden of humanity that everybody should share and we really have to work together on it.
GEORGE ROBERTS: Even the country's president wasn't warned. Yesterday, nearly a week after the announcement, Kevin Rudd called president Susilo Bambang Yudhoyono.
Mr Tantowi again:
TANTOWI YAHYA: Yeah, your Prime Minister made an actions after we made some noise, I mean we made a protest. So the government officials, also member of the parliaments like myself, highly protest on this and then your government did something by calling the president of Indonesia.
I mean it should not happen in the future for the best of the relationship of the two countries in the future.
GEORGE ROBERTS: According to his spokesman Mr Yudhoyono told Mr Rudd that people smuggling is not just one country's problem and stressed the importance of regional cooperation.
A spokeswoman for the Prime Minister confirmed the conversation took place and that president Yudhoyono's version of it is "not incorrect".
Tantowi Yahya is concerned Australia's surprise announcement could see Indonesia dealing with more asylum seekers.
TANTOWI YAHYA: I don't want it to happen but it can happen. Then if it happens then it will add burden that we have right now. Like we have over 10,000 that we have to take care about. When people are with you, you know, you really have to be responsible for them in the name of humanity.
GEORGE ROBERTS: Next year president Yudhoyono's term expires and his party has been polling at below 10 per cent. Any future government Australia deals with is likely to look very different.
Mr Tantowi is from one of the major opposition parties, Golkar, that's already advertising a presidential candidate.
TANTOWI YAHYA: Well I think in the near future, when it comes to Australian policy even though it is local policy, when it creates regional impact, the country, the neighbouring country like Indonesia should always be involved in the conversations or communications.
GEORGE ROBERTS: Next month Indonesia is hosting a forum on asylum seekers and people smuggling to get all countries to work together.
This is George Roberts in Jakarta reporting for AM. ABC Australia