Last week’s suspension of Australia-Indonesia military co-operation has been confirmed as fallout from Indonesia’s internal politics. Indonesian military commander General Gatot Nurmantyo has since “stood on the foot” of President Joko Widodo for diminishing the suspension.

After leading a counter rally to Islamist rioting in Jakarta at the beginning of December, Gatot is now overseeing the paramilitary training of the Islamist group that led the 1 December riot. The Islamic Defenders Front (FPI), which was at the forefront of the December 1 riot, announced on Friday that it had begun receiving training from the Indonesian military (TNI).

The TNI confirmed Sunday that it was training FPI members, but denied that it was providing them with military training.

Photographs from the training program showed FPI members crossing military-style obstacle courses and a TNI officer pinning an award on the uniform of an FPI member. The photos, first released by the FPI, were Sunday published by the respected Indonesian news outlet Tempo. The TNI acknowledged that it was conducting the training, in Lebak Regency, West Java.

Last week, Gatot announced the suspension of Australia-Indonesia military co-operation without reference to either the Defence Minister or President. The suspension was allegedly in response to material offensive to Indonesian national ideology, Pancasila (Five Principles), seen by a TNI special forces (Kopassus) member at the Australian Defence Force Special Air Service Regiment (SASR) base in Perth.

However, within 24 hours, the rationale for the suspension of military co-operation was widened to include references to include Free West Papua material, a critical history of TNI operations in 1965-66 and in East Timor, recruiting Kopassus members as spies and the rotation of US Marines through Darwin. Compiling the list of “offences” after the announcement of the suspension looked increasingly like a pretext for action.

Gatot is from the TNI’s conservative, hardline faction, which wants a more active role for the military in Indonesia’s civilian politics. President Joko Widodo (commonly known as Jokowi) has so far resisted the re-assertion of military involvement in civilian affairs but, weakened, has relied on the TNI to shore up his flailing presidency.

A mass Islamist protest against Jakarta’s Christian-Chinese Governor Basuki Tjahaja Purnama (known as “Ahok”) on December 1, which turned into a riot, was spearheaded by the militant FPI. In response to this assertion of a violent Islamist agenda, Jokowi asked Gatot to lead a counter rally three days later.

Gatot has long been suspicious of outside actors and has not trusted Australia since its UN-sanctioned intervention in East Timor in 1999. Emboldened, and with little respect for either the President or, by past comments, for Indonesian democracy, Gatot acted against Australia.

Gatot had earlier said he had waited for an opportunity to act against Australia and, believing he had acquired the political clout to act unilaterally, did so. However, Defence Minister Ryamizard Ryacudu and Jokowi quickly back-peddled, stating that relations with Australia were, overall, okay. They limited the suspension of military co-operation to language teaching at the SASR barracks in Perth.

Stung by this rebuttal, Gatot has rounded on Jokowi by going from opposing the FPI to supporting them. The TNI has previously had an ambiguous relationship with militant Islamist organisations.

In the early 2000s, the TNI supported Islamist militants, such as by assisting their travel to fight against Christians in Ambon and Sulawesi. This was intended to help destabilise the presidency of Abdurrahman Wahid. The TNI has also taken a leading role in combating Islamist terrorism and been at the forefront of attacks on terrorist hide-outs.

If Gatot believed he had reason not to trust Australia, this was exacerbated on Saturday when a lone protester scaled the walls of the Indonesian consulate in Melbourne and unfurled a “Free West Papua” flag. It appeared that the consulate’s usual security was not on duty on that day.

Indonesia’s Foreign Minister Retno Marsudi described the action as “absolutely intolerable” and demanded that Australia protect Indonesian sovereign offices on its territory. General Gatot is likely viewing this “lack of protection” as a further sign of Australia’s inherent duplicity in bilateral relations.

Australia-Indonesia relations have a long history of difficulties, invariably reflecting the internal dynamics of one or both countries. In particular, Indonesian officials are highly sensitive to questions of national unity and sovereignty and real or perceived challenges are both responded to assertively, if sometimes disproportionately.

Because such questions are so sensitive, they are a touchstone in Indonesian domestic politics. Leveraging political support in Indonesia need only identify a perceived external threat. Anyone who does not immediately get on board thus has weak “nationalist” credentials.

In this, Gatot has Jokowi in a pincer move. He has staked out his own nationalist credentials regarding the “threat” of Australia, which Jokowi has failed to adequately respond to.

And now Gatot has shown that he can manipulate the FPI and its growing mass of Islamist followers to his own ends. Jokowi’s corner is shrinking and, should Gatot choose to do so, Australia may again be used to demonstrate his growing political power.

*Damien Kingsbury is a professor of international politics at Deakin University, Melbourne.