Prime Minister Malcolm Turnbull is repudiating comments made by Deputy PM Barnaby Joyce that seemed to link a trade dispute over cattle to the increase of boats of asylum seekers heading to Australia.

PM Turnbull praised Indonesian President Joko "Jokowi" Widodo as a "great leader" and an "inspirational leader", and made it clear that his government is not accusing the Indonesia government of people smuggling.

"The only point that I want to stress is that our cooperation with Indonesia in terms of stopping people smuggling is very, very strong," said the Prime Minister.  "They are as committed to stopping that trade as we are," Mr. Turnbull added.

For a short time in 2011, Australia suspended its live cattle trade to Indonesia over concerns of cruelty in Indonesian slaughterhouses.  At the ABC regional leaders debate on agricultural and other policies in Gouburn, NSW on Wednesday night, Mr. Joyce became the first Australian politician to  suggest the suspension undermined Indonesia's efforts to stop people smugglers.

"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," said Deputy PM Barnaby Joyce.  "I think it's absolutely the case that we created extreme bad will with Indonesia when we close down the live animal export," he added.

The Indonesian Embassy denied any link between beef trade and asylum seeker issues.  And the matter provided fodder for the opposition in the weeks leading up to the 2 July elections.

"It's a really, really ignorant remark," said Opposition Leader Bill Shorten.  "When he starts weighing into foreign policy, I think he should best leave that to the grown-ups in the room."