A Jakarta think-tank intellectual was once asked whether Beijing listens when Jakarta speaks. He responded emphatically: 'Oh yes! The problem is we don't say enough'.

In the post-authoritarian era, Indonesian officials, like many of their Southeast Asian counterparts, have tended to self-censor when it comes to China, avoiding public criticism while benefiting from considerable Chinese largesse. This is what makes recent public comments by senior Indonesian military officers about the vulnerability of Indonesia's South China Sea-located Natuna Islands so interesting. 

Following a February 2014 trip to Beijing, for example, Indonesian Armed Forces (TNI) commander General Moeldoko signaled enhanced defence measures for the Natuna Islands. 'Since Natuna is strategically located, the increase of its forces at sea, on the ground, and in the air is necessary to anticipate any instability in the South China Sea and serve as an early warning system for Indonesia and the TNI', he explained.

Then in March, Air Commodore Fahru Zaini, based at Indonesia's Coordinating Ministry for Political, Legal and Security Affairs, publicly stated that 'China has claimed Natuna waters as their territorial waters. This dispute will have a large impact on the security of Natuna waters'. 

In June 2013, Commodore Amarullah Octavian was even more frank. In announcing that Indonesia would host 'Exercise Komodo' he explained that 'the exercise will focus on naval capabilities in disaster relief, but we will also pay attention to the aggressive stance of the Chinese government by entering the Natuna area'.

Unsurprisingly, such candid public comments by senior Indonesian military officers did not go unnoticed in the Indonesian press and scholarly community.

There was a particularly interesting exchange on this issue between Indonesian security analyst Evan Laksmana and American academic Anne Marie Murphy. Murphy had interpreted the TNI comments as evidence of a significant policy shift by Indonesia and described the 'public declaration' of a maritime conflict with China as a 'potential game changer'. 'The strategic ambiguity that has allowed Indonesia to position itself as a mediator between China and its ASEAN neighbours has been lost', she concluded.

Laksmana was quick to counter, citing statements by Foreign Minister Marty Natalegawa and foreign ministry spokesman Michael Tene, who clarified there was no territorial dispute between Indonesia and China. According to Laksmana, Air Commodore Zaini was speaking neither for the Indonesian government nor TNI. Laksmana said there was no policy shift and that 'the status quo between China and Indonesia over the Natunas will remain until the day Beijing challenges Indonesia's rights to explore the natural resources within our EEZ'.

Ultimately, Laksmana is correct. There is no formal policy shift by Indonesia on the South China Sea. But Murphy's analysis is not erroneous. There may be no formal shift, but the recent unguarded comments by senior TNI officers, and the subsequent 'clarification' from senior diplomats, can be understood as the public manifestation of civil-military differences over China. 

TNI, like all militaries, is essentially realist in orientation. Its builds forces and plans strategy based on a range of threat scenarios. Indonesia's defence planners have factored in a potential Chinese threat to the Natuna Islands since the mid-1990s. Former armed forces commander General Wiranto reflected the military's contrived ambivalence about a China threat in 1996: he denied that Indonesia's then-largest joint exercise around the Natuna Islands was in response to a China threat, but added that he 'could not help it if there were observers who chose to see it that way'.

Indonesia's foreign ministry, by contrast, is more liberal-institutionalist in inclination. It pursues Indonesia's national interests through diplomacy and a strong predilection for multilateral solutions to regional security problems, mainly through ASEAN-centred mechanisms. Unlike their TNI colleagues, who prepare for the worst, the civilian diplomats are keen to preserve Indonesia's official impartiality on South China Sea disputes, which provides Jakarta with added influence and leverage with Beijing. 

Beneath Laksmana and Murphy's 'policy continuity' versus 'policy shift' debate, one can see the internal dimensions of rising strategic uncertainty playing out in differences between the foreign ministry and TNI. Expect such differences to become more commonplace as Beijing further infringes on Indonesia's territorial sovereignty. Such infringements will both test Jakarta's formal impartiality on South China Sea territorial disputes and challenge Indonesia's domestic consensus on the need to subordinate strategic concerns about China to higher economic and foreign policy objectives.