To suggest that Australia’s relationship with Indonesia has been marked by periods of instability would be less accurate to say the otherwise unstable relationship has been marked by brief periods of stability. After a few years of good relations, it again appears that Australia is headed into difficulties with its near neighbour.

Always highly sensitive around issues of sovereignty, Indonesia’s Foreign Minister Marty Natalegawa has rejected the newly elected Abbott government’s policy of paying villagers for information about people smugglers. He has also rejected the Coalition’s otherwise poorly conceived policy of buying potential people-smuggler boats.

Indonesia had already strongly signalled its opposition to the Coalition government’s policy of “turning back the boats” (“where safe to do so”). Its view is that, once boats are in international waters, they are not Indonesia’s responsibility, nor does it have the capacity to assist boats that might get into difficulties.

These new difficulties in the relationship result directly from a significant change in Australia’s foreign policy being announced as an election promise without first having been negotiated with the principal affected party. As the incoming Coalition government is quickly learning, there is a big difference between populist pre-election promises and post-election international realism.

Similarly, comments by senior Nationals member Barnaby Joyce that he will oppose the sale of Australian agricultural land to Indonesia to raise cattle for the Indonesian market will cause long-lasting offence in Indonesia. Indonesians will rightly point out that Australia has significant investment in mining and other industries in Indonesia, but hypocritically does not wish that investment right to be reciprocal.

Australia has enjoyed several years of generally untroubled relations with Indonesia. The relationship is officially described, on both sides, as the best it has ever been. That is probably correct.

However, a very large part of that positive relationship has been a result of the benign and pro-Western leadership of President Susilo Bambang Yudhoyono. This has been assisted by the previous two governments’ more nuanced diplomacy towards Indonesia.

Under the surface, however, many of the longer-standing tensions and suspicions about Australia’s intentions and attitudes have remained among many senior Indonesians politicians. These suspicions, they believe, are now rapidly being confirmed.

The incoming government’s “bull in a china shop” approach to regional diplomacy was always going to test Indonesia’s patience. For senior Indonesians, and indeed many others, how one is seen to act is as important as the act itself.

But more importantly, any new tensions in the relationship will likely spill into Indonesia’s forthcoming electoral period. Yudhoyono steps down at the end of his second term next year, and his successor is much less likely to be as understanding or accommodating of Australia’s interests.

Indeed, there remains a good possibility that Indonesia’s next president will run a distinctly “nationalist” agenda, which will almost by definition be combative towards Australia. As Indonesia’s economy continues to grow strongly and its strategic value only develops in importance, how Australia engages will become increasingly critical.

Australia has long acknowledged that its future lies in closer engagement with Asia, confirmed yet again by the Asia century white paper. Good relations with Indonesia are central to that engagement. Australia’s new government would do well to remember that, and to act accordingly.

*Professor Damien Kingsbury is director of the Centre for Citizenship, Development and Human Rights and is the author and editor of a number of books on Indonesian politics