The government said it has now turned back 633 asylum seekers who were trying to reach Australia by boat.
In July a small wooden boat, the first "illegal" vessel entry into Australia since June 2014, was spotted off the north-west coast.
It was not seen again and the government refused to say where it was.
The government usually refuses to comment on boat turn-backs but Immigration Minister Peter Dutton on Thursday told local media: "There were 46 people on a recent venture that did come from Vietnam; we have negotiated their return to Vietnam."
"The boat that they came on has been scuttled and we have been able to stare down that venture," he said, adding that the government's policy was not to allow people arriving "illegally" by boat to settle in Australia.
Australia has been sending migrant boats back to where they came from since December 2013.
Refugee support group VOICE said three of the Vietnamese refugees were now in police detention in Vietnam.
Spokesman Trug Doan told the Australian Broadcasting Corp they were being held "for an indefinite period for interrogation".
The Greens party has said the turn-backs are a breach of the UN's Refugee Convention.
Greens Senator Sarah Hanson-Young said last month that handing the Vietnamese group back to Vietnam would be refoulement - the expulsion of people entitled to claim refugee status.
Australia has confirmed it sent 46 asylum seekers back to Vietnam after intercepting their boat off the coast of Western Australia last month.