Jakarta has rejected comments by Barnaby Joyce linking the halt on live cattle exports to Indonesia and asylum-seeker boat arrivals in Australia as "simply not true".
Deputy Prime Minister Barnaby Joyce has started the day trying to downplay comments he made on Wednesday night, saying he meant that the controversial suspension of the live cattle trade to Indonesia in 2011 made it difficult to negotiate with them on the issue of asylum seekers.
Ministry of foreign affairs spokesman Arrmanatha Nasir 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 area.
The issue of the suspension of live cattle was unrelated and there "is no link."
Mr Nasir noted it was election time in Australia and that Foreign Minister Julie Bishop had commented on Mr Joyce's statements on Thursday morning, also stating there was no link.
The Indonesia Institute in Western Australia on Thursday described Mr Joyce's comments as "wrong".
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, but it had nothing to do with an increase in asylum seekers heading from Indonesia to Australia.
"Whilst Indonesia will not be pleased by Mr Joyce's comments, Indonesia ... understands that what is said during a robust election campaign should not necessarily be seen as formal policy of the Australian government's position," the organisation said in a statement.
"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 bilateral relationship on track."
Mr Joyce linked the two issues during a regional debate on Wednesday night in Goulburn, saying: "When we closed down the live animal export industry (to Indonesia), it was around about the same time that we started seeing a lot of people arriving in boats in Australia."
On Thursday morning, he clarified his comments, saying the ban on exports hampered talks with Indonesia on people smuggling.
