Indonesia rejects Joyce's comments

"Flawed", "patently false" and "simply not true".

These are the descriptions coming out of Indonesia following comments made by Barnaby Joyce linking the 2011 suspension of live cattle exports with an increase of asylum seeker boats to Australia.

The deputy prime minister has come under fire both in Australia and Indonesia over comments he made during a regional debate on Wednesday night in Goulburn, linking an increase in boat arrivals to the country's shores to the halting of the live cattle trade.

He sought to downplay the remarks on Thursday by saying the ban on live exports made negotiations with Indonesia more difficult.

But former Indonesian foreign minister Marty Natalegawa who discussed both subjects with Australia's then prime minister Kevin Rudd, rejected the comments, saying any suggestion a link existed between the two issues is "fundamentally flawed and patently false".

"At best it represents an over analysis of the subject ... Worse still, it is shocking to suggest that the Indonesian government would put at risk the safety and lives of innocent asylum seekers in making the treacherous journey to Australia simply to make a point," he told AAP in a statement.

Dr Natalegawa added that the Indonesian government had "constructively discussed" the two matters with Australia, which were eventually resolved.

Ministry of Foreign Affairs spokesman Arrmanatha Nasir also told AAP on Thursday that to "suggest there is any link is simply not true".

"Indonesia and Australia have been working on the issue of irregular migration ... in a comprehensive manner through the Bali Process."

He said Indonesia has been a "responsible country" in this space and their commitment on the issue of people smuggling "can't be questioned".

While it was a "pity" Mr Joyce made the comments, Mr Nasir noted Australia was in the middle of an election campaign and also pointed to Julie Bishop's comments dismissing any link between the two issues.

The Indonesia Institute in Western Australia has also described Mr Joyce's comments as "wrong".

While they said the cancellation of live cattle exports without consultation with the Indonesian Government had an immediate impact on meat prices and caused tensions between the two countries, it had nothing to do with an increase in asylum seekers heading from Indonesia to Australia.

"We can only hope that Indonesia will simply shrug-off Mr Joyce's comments as part of the robust election process, and thus keeping the now much improved bi-lateral relationship on track," the organisation said in a statement.