SYDNEY/JAKARTA (Reuters) - Indonesia and Australia sought to calm tensions on Thursday after Indonesia's military said it had suspended cooperation because of "insulting" teaching material found at an Australian base that questioned Jakarta's sovereignty in Papua province.
A day after the shock announcement by Indonesia's army chief, which seemed to blindside not only Australia but parts of President Joko Widodo's government, there was still confusion over the status of ties between the Asia-Pacific neighbours.
The countries have extensive military cooperation, which ranges from counter-terrorism cooperation to border protection,
President Widodo said ties with Australia were "still in a fine condition" and his defence minister and military chief had been asked to investigate.
"We have agreed, Indonesia, Australia, to respect each other, to value each other and not meddle in each other's domestic affairs," Widodo said.
There were still, however, contradictory messages.
Indonesia's chief security minister Wiranto said only cooperation related to the military's Australia-based language training program had been suspended.
But a statement from the office of Indonesia's state secretary said joint training, exchange of officers and bilateral visits had also been suspended.
Earlier, Indonesia's Armed Forces Chief Gatot Nurmantyo said training with Australia had been suspended and other areas of cooperation were being re-evaluated pending an investigation.
Australian Prime Minister Malcolm Turnbull said he looked forward to the matter being resolved "as soon as possible".
"I acknowledge and value President Widodo’s commitment to the strategic partnership between our two countries and value our personal friendship," Turnbull said in a statement.
The neighbours have had a rocky military relationship in recent years. Australia stopped joint training exercises with Indonesian special forces (Kopassus) after accusations of abuses by the unit in East Timor in 1999, as the territory prepared for independence.
Ties resumed when counter-terrorism cooperation became imperative after the 2002 nightclub bombings on the resort island of Bali that killed 202 people, including 88 Australians.
Indonesia most recently suspended military ties in 2013 over revelations that Australian spies had tapped the mobile telephone of then president Susilo Bambang Yudhoyono.
Nurmantyo said on Thursday that "unethical" teaching material had been found by an Indonesian officer who had been sent to Australia to teach.
The material "discredited the Indonesian military (TNI), the nation of Indonesia and even the ideology of Indonesia," he said, referring to material concerning East Timor and "Papua needing to be independent", as well as mocking the country's founding principles, known as Pancasila.
Papua, where a separatist movement has simmered for decades, is a sensitive issue for Indonesia, which took over the former Dutch colony after a widely criticized U.N.-backed referendum in 1969.
"That curriculum had been used for a long time," Nurmantyo said, noting it had now been removed.
Australian Defence Minister Marise Payne said an investigation into the teaching materials, found at Campbell Barracks in the west Australian city of Perth, would be concluded "imminently".
She denied allegations, reportedly made by Nurmantyo in a lecture last year, that Australia had tried to recruit Indonesian soldiers as agents during training.
Payne said Jakarta has given no indication of any change in helping Australia to enforce its controversial immigration policy, which includes turning back boats carrying asylum seekers.
Additional reporting by Tom Westbrook in SYDNEY and Bernadette Christina Munthe and Agustinus Beo Da Costa in JAKARTA; Writing by Fergus Jensen and Ed Davies; Editing by Bill Tarrant