John Kerin – Indonesia's notorious Kopassus special forces soldiers are eager to resume counter-terrorism training with the Australian military and do not understand lingering concern about their alleged brutality or links to terrorist groups, a parliamentary inquiry has heard.

However, some resentment remained within Kopassus over Australia cutting ties with it six years ago, Defence Department deputy secretary Shane Carmody told the inquiry. This was related to the unit losing valuable training opportunities rather than Australia's concerns about Kopassus's human-rights record.

"At the special forces level, certainly they [Kopassus] have felt quite keenly that we have not worked with them since 1997, and they have seen a diminution of their skills," Mr Carmody, who returned recently from a visit to Indonesia, told the inquiry into Australia's relationship with Indonesia. "[But] the soldiers are saying, 'We don't know what all the fuss is about, let's get on with it' [resuming ties]."

The federal Government has been criticised over plans to begin limited exercises with Kopassus to deal with hostage and hijack situations in response to a heightened threat to Australians from terrorism in the archipelago. Australia cut its ties with Kopassus after the special forces were implicated in killing political activists in the dying days of former president Suharto's regime. Kopassus-trained militia also fired on and wounded Australian soldiers in the lead-up to East Timor's independence in 1999. Elements of Kopassus are also suspected of training terrorist groups such as Laskar Jihad.

Other senior Australian military officials, including army chief Peter Leahy and special forces chief Duncan Lewis, have also visited Indonesia since June in a bid to smooth the way for a resumption of ties. Mr Carmody said renewing ties was crucial because "if something happened tomorrow it would be inappropriate for our special forces and the Indonesian special forces to meet for the first time in a hangar five minutes before the assault". "Our view is we need to try and find ways to build a very narrow relationship in [counter-terrorism]," he said. A defence submission to the inquiry has suggested that lingering misunderstandings over Australia's 1999 East Timor intervention are hampering efforts to resume defence ties between the two countries.

But Opposition foreign affairs spokesman Kevin Rudd, who has just returned from Indonesia, said Australia had an alternative to working with Kopassus. He said the US Government, which had concerns about Kopassus's involvement in the killing of US citizens in Papua last year, was building a counter-terrorism capacity within the Indonesian national police. He said it was devoting $45 million to developing a 300-strong counter-terrorism unit within the police force. "The [Australian Federal Police] has developed an excellent relationship with the Indonesian national police and it is the police that Australia should also be developing its counter-terrorism ties with," he said.