Malcolm Turnbull has declared Australia's relationship with Indonesia has never been better, after his deputy with an increase in asylum-seeker boat arrivals.
Appearing beside Mr Joyce at a press conference in Rockhampton, Mr Turnbull stepped in when journalists quizzed the Deputy Prime Minister about the comments.
Mr Turnbull insisted there was no link between the Indonesian government and people smuggling.
Mr Turnbull "There is no link between the Indonesian Government and people smuggling" and praised Indonesian President Joko 'Jokowi' Widodo.
"We have a good relationship with them. I think President Jokowi is a great leader, he's in fact an inspirational leader," Mr Turnbull said.
"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."
But Labor's temporary ban in 2011 was an "outrageous affront" to Indonesia, he told reporters in Rockhampton.
Mr Joyce attempted to clarify the comments when speaking to Channel Seven on Thursday morning.
"I'm not saying that this caused the Indonesians to start sending people across, I never suggested that," he said.
"But I did clearly suggest that it made it difficult, gave a real degree of difficulty in how we negotiate with Indonesia."
Mr Joyce is under fire from Labor, the Greens and the man challenging him in the seat of New England.
"This is politics of the worst kind," Tony Windsor said, labelling the remarks as reckless and offensive.
Labor backbencher Nick Champion told Sky News: "It's hard to believe this man is deputy prime minister."
Joyce's comments were slammed by Opposition leader Bill Shorten who called them "really ignorant remark".
"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," Mr Shorten said.
"But when he starts weighing into foreign policy, he should best leave that to the grown-ups in the room."
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