He says some refugees who were potentially destined to leave detention under the arrangement with the US are saying they would rather go to New Zealand.
"We don't want to disrupt the arrangement we have got with the US," Mr Dutton told Sky News on Sunday.
"We don't want people hopping on boats thinking they can get to New Zealand, stay there for a couple of years, become a citizen and then come to Australia."
He said Australia's border force had already stopped four vessels coming across the Torres Strait that were on their way to New Zealand.
"We have to be mindful that the risk has not gone away," he said.
He said Mr Shorten was "clearly working on" a secret policy that would be announced after the next election if they win.
"Australians don't want the people smugglers back in control over who comes to this country," he said.