Foreign Minister Julie Bishop has contacted the Indonesian government after Deputy Prime Minister Barnaby Joyce's comments linking the live export ban to asylum seekers arriving in boats.
The Department of Foreign Affairs and Trade confirmed to SBS News Ms Bishop had spoken with "Australia's Ambassador in Jakarta and directly with Indonesia's Foreign Minister" but did not give further details about who she spoke to or what they discussed.
Mr Joyce came under fire after suggesting during a regional leaders' debate in Goulburn on Wednesday night that Labor's 2011 ban on live cattle exports to Indonesia was linked to the arrival of asylum seekers of boats.
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"Might I remind you when we closed down the live animal export industry, it was around about the same time that we started seeing a lot of people arriving in boats in Australia," Mr Joyce said.
Mr Joyce's comments prompted an immediate response from mediator Chris Uhlmann who asked, "Do you realise you are suggesting the Indonesian Government then unleashed the boats in response?".
"I think it's absolutely the case that we created extreme bad will with Indonesia when we closed down the live animal export," Mr Joyce said.
"I suggest the Greens and Labor Party created immense bad will and [the number of refugees coming] was affected."
Prime Minister Malcolm Turnbull today dismissed suggestions there was a link between the live export ban and the increased arrival of asylum seekers.
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"There is no link between the Indonesian Government and people smuggling," he said.
"We have a good relationship with them. I think President Jokowi is a great leader, he's in fact an inspirational leader.
"The only point that I want to stress is that our cooperation with Indonesia in terms of stopping people smuggling is very, very strong.
"They are as committed to stopping that trade as we are."
Opposition Leader Bill Shorten slammed Mr Joyce's remarks, labelling them "really ignorant".
"It's one thing if he wants to have a fight with Johnny Depp about his wife's dogs Boo and Pistol, that sort of just makes us a figure of fun," he said.
"But when he starts weighing into foreign policy, he should best leave that to the grown-ups in the room."
Indonesia's foreign affairs ministry lablled the comments as "simply not true".
"Indonesia and Australia have been working on the issue of irregular migration ... in a comprehensive manner through the Bali Process," spokesman Arrmanatha Nasir told AAP.
He said Indonesia has been a "responsible country" in this area.
- with AAP