Concerns regarding Australian military teaching materials and remarks uncovered late last year have placedstrain on relations with Indonesia. The strange affair of our on-again-off-again defence cooperation arrangements with Indonesia continues to confuse most observers.

It began with a statement by the spokesman for the commander of Indonesias armed forces, General Gatot Nurmantyo, that defence cooperation with Australia had been suspended for technical reasons.

These were later revealed to be complaints made late last year by an Indonesia Special Forces (Kopassus) member working as a language trainer in military courses in Perth. He had complained that certain materials dealing with Indonesia used by the Australian Defence Forces (ADF) were offensive.

It is still not entirely clear what the material was. Different accounts say it related to the status of West Papua or the role of the late General Sarwo Edhie Wibowo in the 1965 killings; or that it denigrated the national ideology, Pancasila, by calling it panca_g_ila (gila means crazy). Or perhaps it included all of these.

In any case, Nurmantyo raised the matter with a letter to his Australian counterpart in early December and the ADF initiated an inquiry, which is yet to produce a report. Nurmantyo seems to have been unhappy with progress and decided to make the matter public, sparking much excitement in the Australian media.

Things then became more confusing. Nurmantyos announcement was followed by comments from the spokesman for Indonesian President Joko Widodo (Jokowi) that he had not been consulted but thought it was all exaggerated. Soon after, however, Jokowi told reporters that he endorsed Nurmantyos decision as a matter of principlepresumably a reference to defending_Pancasila_. He added that no specific timetable existed to restore military ties but, oddly, relations with Australia were somehow just fine.

Australian Defence Minister Marise Payne, scrambling to get a grip on the situation, issued a statement that the inquiry was underway, efforts were being made at military and political levels to resolve the matter and that only some training activities were affected. This was quickly countered by Nurmantyo, who said it was, in fact, a much wider suspension of cooperation.

If this had been true, it would have meant that the head of Indonesias armed forces, a serving general, had been able to make a decision affecting relations with a foreign power that should be exclusively the right of his superiors in Indonesias civilian governmenta very worrying development.

Paynes position was, however, finally supported by former General Wiranto, Indonesias powerful Coordinating Minister of Politics, Law and Security. Apparently slapping down Nurmatyo, he said that the suspension was, after all, limited to just language training courses.

At the time of writing it was still not completely clear exactly how serious the consequences of all this are for military cooperation between Australia and Indonesia, with some suggesting that it may still affect joint naval exercises scheduled for February.

Whatever the outcomeand it may not be clear for weeks or monthsthe whole perplexing episode does make some things clear, underscoring some hard truths about the Australia-Indonesia relationship.

First is a reminder of the messy nature of policy making in Jokowis Indonesia.

Jokowi is a weak president. A provincial outsider, he is the first president of Indonesia not to lead his own party and has struggled since his election to build support among the elites. He has only recently consolidated a workable political coalition and still struggles to get his agenda through the national legislature, let alone implemented on the ground.

His administration has been dogged by lack of discipline and poor internal coordination, so policy on the runemerging chaotically from conflicting and often attention-seeking statements by high state officialsis unfortunately not unusual. This episode shows that we need to be patient when controversies arise and allow time for Jakarta to sort out its real position.

Second, it reminds us that the relationship is inherently volatile. We are close neighbours, and Indonesia has long had brittle relationships with all its neighbours. In fact, Malaysia and Singapores relations with Indonesia are just as difficult as ours. Tensions are inevitable and we should not panic at the first sign of trouble.

Third, the relationship is becoming harder to manage under Jokowi. There are many reasons for this, but they include rising nationalism in Indonesia. A sort of prickly, defensive nationalismparticularly towards the Westis to be expected in countries that fought to win independence from European colonialism. It has never been entirely absent in Indonesia.

This was moderated somewhat by former president Yudhoyonos internationalist orientation and his efforts to present Indonesia as a good world citizen. Intense competition between Jokowi and former general Prabowo Subianto in the 2014 election campaign quickly ratcheted up public nationalist rhetoric, however.

Ultra-nationalists like Nurmantyo, who does have some history of promoting conspiracy theories about foreign intervention and covert proxy wars in Indonesia, do not seem as out of place as they might have a few years ago. We need to be aware that its leaders are now more likely to take offence over trivial matters, such as training materials in a language course, if they are perceived as a slight to national pride.

Fourth, Australia no longer has a special friend in the palace. This is not to say that Jokowi is hostile to Australia, rather he is indifferent. For whatever reason, Yudhoyono was generally much more enthusiastic about Australia. Yes, he suspended defence, intelligence and people smuggling cooperation when he felt Australia had breached his trust by tapping his phone, but he clearly valued the bilateral relationship and often responded positively to Australian requestseven when it cost him political capital.

Jokowi, by contrast, was unmoved by the huge effort the Australian government undertook to save Australian drug offenders Myuran Sukumaran and Andrew Chan, which he dismissed as foreign interference. Jokowi is an embattled leader, dealing with challenges from within the elite and the rising power of Islamist hardliner groups like the Islamic Defenders Front. The bilateral relationship with Australia is well down his list of priorities.

Fifth, there are number of flashpoint issues that can always be relied on to disrupt the bilateral relationship. They include, among others: the status of West Papua with, as most Indonesians suspect, many Australians favouring the independence of Papua, which is predominantly Melanesian and Christian, unlike most of Indonesia; the loss of East Timor, still painful for many Indonesians, particularly in the armed forces; human rights concerns including, for example, capital punishment and the 1965-6 massacre of Leftists in which General Wibowo was involved; people smuggling; and military and intelligence activity in the region.

These are contentious issues because of different values in some cases (for example on capital punishment) and in others because of different understandings of history (for example, about West Papua). All, however, are aggravated by rising nationalism in Indonesia and rising anxiety about the Muslim world in Australia.

Sixth, our relationship with Indonesiaand our capacity to resolve inevitable tensions in the bilateral relationshipis not likely get much better in the years ahead. Even as our expertise on Indonesia declines, with Indonesian studies fast evaporating in schools and universities, Indonesia sees itself as rising: an emerging world player, economically and strategically.

It is the giant of Southeast Asia, with a population of 270 million, 10 times bigger than we are. All the rating agencies claim that Indonesiadespite its best effortswill be in the top 10 economies by 2030 and in the top 5 by 2050, transforming the region.

Whether this is true or not, Indonesias leaders believe it. They are also well aware that their sprawling archipelagic nation will be of vital strategic importance if war erupts in the South China Sea.

This means that, like it or not, things have shifted between Australia and Indonesia and Jakarta now sees us as the junior partner in the bilateral relationship. Even friendly opinion-makers there often ask why their country should care what Australia thinkswhy do we matter?

Rightly or wrongly (and often it is not our fault), it will be up to us to take the initiative to repair relations when things go wrong. Many Australians will, understandably, greatly resent this, but it is not a matter of fairness or reasonableness, just realpolitik.

The hard truth is that in the years ahead, keeping the bilateral relationship with Indonesia stablefor our own benefitwill, unfortunately, require Australia to work much harder to keep things nice, and perhaps more than it should.

Tim Lindsey is Redmond Barry Distinguished Professor and Malcolm Smith Professor of Asian Law at the University of Melbourne Law School where he directs the Centre for Indonesian Law, Islam and Society.

This article was first published by The Australian Institute of International Affairs on 26 January 2017.