She also announced last month New Zealand would give $3 million to help with the refugees, which is understood to have offended the Australia Government.
Joyce said that Australia had a tough policy on boat arrivals to stop the thousands of arrivals and over 1000 drownings of people.
"That can't go on and it did stop and that's precisely what we wanted," Barnaby Joyce told Larry Williams.
Asked if New Zealand should back off, he said: "I think it's best if you stay away from another country's business. I find that's because others will return the favour at a time that is opportune to them."
"Let's respect countries'' sovereignty and let the sort out their own issues," he said.
"And if you are going to talk to them at all, talk to them quietly and discreetly, off the record, not via telephone, not via TV."
Joyce also spoke about the citizenship furore that forced him to resign from Parliament after discovering he was a New Zealand citizen.
He has since given up that citizenship and won a byelection to return to Parliament with an increased majority.
Australia's Constitution bars dual citizens from holding office but this year a glut of MPs have had to resign after discovering they were citizens of other countries, often without realising it.
Joyce said the revelation he had New Zealand citizenship because his father was from New Zealand had caught him off guard.
He also referred to a staffer in Labor MP Penny Wong's office contacting Labour MP Chris Hipkins in the lead-up to that discovery, saying "during that time they were digging round to try and make sure they could get me booted out."
Asked if he believed there was collusion, he said it had been confirmed the two had talked and now Prime Minister Jacinda Ardern had "chipped" [reprimanded] those involved over it: "so what other evidence do you need?"
Hipkins has maintained he did not know Joyce was the subject of his discussion with Wong's staffer Marcus Ganley but it did prompt him to lodge parliamentary questions asking about the citizenship status of a person born to a New Zealand father.
Those questions combined with media questions to New Zealand officials prompted officials to look into Joyce's citizenship and advise him he was a citizen.
Then freshly elected as Labour leader, Ardern reprimanded Hipkins for his involvement, saying it was inappropriate to get involved in the matter and she had not known about it – but it earned a rebuke from Australia's Foreign Minister Julie Bishop who had said she would find it hard to trust a Labour Government in New Zealand if they won the election.
Bishop has not apologised, but has since said she accepted Ardern's statement that she had not known, and that it was inappropriate.
Joyce has given up his New Zealand citizenship and won the byelection for his Tamworth seat to get back into Australia's Federal Parliament with an increased majority.
He said the section of the Constitution which required MPs to only hold Australian citizenship should be amended but that would require a referendum. "It's not an easy task but overwhelmingly people think this is absurd."
He said his father had come out of New Zealand in 1947 after World War II and the law had been changed in 1949 "so unbeknownst to him he was a New Zealand citizen between 1949 and 1978 and during that time I was born."
Joyce laughed when told he had been nominated for New Zealander of the Year, saying "a lot of people had a lot of fun at my expense."
"New Zealand is a great country and I'm very proud my grandfather was a Lieutenant Colonel in the Anzacs there for New Zealand."
