On his first foreign trip since ousting Julia Gillard barely a week ago, the Australian leader will meet with President Susilo Bambang Yudhoyono to tackle a subject that will be key in upcoming elections.
Despite Canberra's tough new policies banishing asylum-seekers to remote Pacific islands, thousands of would-be refugees continue to make the sea crossing to Australia, often from transit hubs in Indonesia.
Many have died trying to make the hazardous journey in crammed, rickety boats, normally after paying huge fees to people-smugglers.
Although he is under pressure to take a tough stance on the election campaign hustings, Rudd cautioned against expecting major outcomes from the talks as he arrived in Jakarta late yesterday.
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"We have been consistent in saying that this problem cannot be solved by one country," he said.
"It needs a joint effort from destination and transit countries, as well as countries of origin."
Rudd insisted that "the full breadth of our relationship" would be discussed during the trip. At a breakfast event with business leaders in Jakarta today, he sought to turn the focus of the visit to trade.
"Already Indonesia's consuming class is larger than Australia's population," he said.
Rudd also sought to ease tensions surrounding live cattle exports, which have become a major point of conflict in trade relations between the neighbours.
Australia halted shipments to Indonesia in 2011 after TV footage showed harsh treatment of animals in the country, a move that badly hit the industry in Australia. Shipments have since resumed but in far reduced numbers.