The rupture — over training material deemed insulting to Indonesia’s founding ideology that had been found on a military base in Australia — has highlighted the political challenges Indonesia’s president, Joko Widodo, has faced in recent months as he confronts threats to his power ahead of elections in February.
Questions are being raised about whether Mr. Joko, widely known as Jokowi, knew that his top general was planning to suspend military ties with Australia. The general, Gatot Nurmantyo, is an ardent nationalist who is thought to have political ambitions of his own.
The suspension of military ties with Australia threatened Indonesia’s efforts to improve relations with its southern neighbor and raised the specter of a deep split between the two countries, both vital American allies in the region.
In a news conference Thursday night, Indonesia’s chief security minister said the suspension of military cooperation, announced earlier in the week, was limited only to language training, which remained suspended. The minister, Wiranto, stressed that “the bilateral relationship of both countries is running well.”
“It does not mean the breaking of our defense cooperation fully,” he added. Mr. Wiranto, like many Indonesians, goes by one name.
The confusing signals from Indonesia’s military come as Mr. Joko faces stark shifts in the nation’s political landscape amid the falling fortunes of his protégé, Basuki Tjahaja Purnama, the governor of Jakarta, Indonesia’s capital. Mr. Basuki, also known as Ahok, was widely considered a potential running mate for Mr. Joko’s re-election effort in 2019.
But Mr. Basuki, an ethnic Chinese Christian, is fighting blasphemy charges and faces jail after large Islamist-led rallies against him, potentially hurting his hopes in February of becoming the first non-Muslim to be elected governor of Jakarta. He inherited the governorship from Mr. Joko after Mr. Joko won the presidency in 2014. A defeat for Mr. Basuki in court could spell trouble for Mr. Joko in 2019.
“Up until September, everything seemed calm for Jokowi,” said Philips J. Vermonte, executive director for the Center for Strategic and International Studies in Jakarta. “Re-election was assured. And then the storm came, and that storm was in a package called Ahok.”
The turmoil could have provided a political opening for General Gatot by publicly breaking with the Australian military over an issue of national honor. Officials said the suspension in military cooperation was precipitated by the discovery on an Australian training base of materials that apparently disparaged Pancasila, Indonesia’s founding state ideology, which mandates belief in monotheism and unity among Indonesia’s 250 million people.
General Gatot, who has positioned himself as a defender of Indonesia, is widely thought to have political ambitions of his own. He is deeply suspicious of China and the United States. He has publicly mused that food shortages in China may send waves of hungry Chinese southward toward Indonesia. He has also claimed that the cause of gay rights amounts to a proxy war by Western interests to erode Indonesian culture.
“It is a public secret that Gatot has political ambitions, and it will be a challenge for Jokowi to manage them as we approach the 2019 polls,” said Marcus Mietzner, an associate professor who studies Indonesian politics and the military at the Australia National University in Canberra, the Australian capital.
“Gatot senses that his views are now falling on fertile ground, and that emboldens him further,” Mr. Mietzner added.
Publicly, Mr. Joko stood by his general’s decision to suspend military ties, calling it a “matter of principle.”
But Mr. Mietzner said Mr. Joko’s government, already tested by the huge rallies against Mr. Basuki, would be eager to put the flare-up with Australia to rest.
“No doubt there will be serious discussions within the Indonesian government about how such a momentous diplomatic decision could have been taken by the head of the armed forces without involving the political leadership,” Mr. Mietzner said.