Australian Defence Minister Marise Payne reacts during a media conference, regarding Indonesia’s military suspension with Australia, in Sydney, Australia, January 5, 2017. AAP/Mick Tsikas/via Reuters

Defence Minister Marise Payne has recently denied the claims that Australia recruits Indonesian military officers as agents or spies. Payne also said that the country is handling the suspension of military ties between the two countries and is hoping that the differences will be resolved soon.

As revealed earlier this week, Indonesian military suspended ties with its Australian counterpart without the involvement of President Joko Widodo or his defence minister. The move came after an Indonesian special forces trainer claimed that he found offensive material at a military base in Perth. The material was understood to be documents suggesting that West Papua should be given independence as it was a part of Melanesia and ridiculing Indonesia's national ideology, Pancasila.

This outraged military chief General Gatot Nurmantyo who said in his speech in November that Australia sought to "recruit" country’s best and brightest as sources. “Every time there is a training program, like recently, the best five or 10 students would be sent to Australia. That happened before I was chief so I let that happen,” he had said.

Senator Payne has recently denied of the allegations made. However, she said that the matter was of significant concern to the nation. “We have indicated our regret that this occurred and that offence was taken,” she stated in a press conference on Thursday. About the offensive material being found at the military base, she said that inquiry is underway and “close to finalisation.”

“I would hope at the conclusion of the inquiry, when we're able to indicate to Indonesia the steps that have been taken in Australia to address any of these concerns, we'll be able to discuss resuming the relationship across the board then,” she said.

The dispute is spoiling the defence relations between the countries. A trip of Indonesian military staff college students to Australia was cancelled recently. Furthermore, Indonesia's participation in a forthcoming multi-national naval exercise is also in doubt.

Despite the hostile allegations from the General Nurmantyo, Payne praised him and said that she has a great deal of respect for him and the way he works for the military. She is hoping for a speedy resolution.