A group of Vietnamese asylum seekers were held secretly at sea for more than a month before being sent back to their home country, the commander in charge of Australia's border operations has revealed.

Operation Sovereign Borders head Major General Andrew Bottrell told a Senate estimates hearing the group of 46 asylum seekers was intercepted on March 20, 2015.

The group of men, women and children were taken into Australian custody and held at sea until April 18.

Officials told the estimates hearing they had face-to-face interviews at sea and were "screened out", meaning none of those on board engaged Australia's protection obligations.

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They were taken back to Vietnam on the Australian navy ship HMAS Choules.

"The amenity that was provided to the 46 was quite suitable," Major General Bottrell said.

"They had access to appropriate medical care, food, accommodation and ablutions of quite a high standard."

Labor senator Kim Carr questioned the officials about whether the group was effectively held on an Australian "prison ship".

Immigration and Border Protection Department secretary Michael Pezzullo rejected the description.

"Those vessels, I don't think by any commonsensical or reasonable definition could be described as a prison ship," Mr Pezzullo said, arguing none of the asylum seekers had been convicted of a crime.

Major General Bottrell told the hearing Australia had a written assurance from Vietnam that provided a "level of comfort" about returning the group.

"[There was] an assurance from the government of Vietnam that there would be no retribution for their illegal departure from Vietnam," he said.

Greens immigration spokeswoman Sarah Hanson-Young questioned the officials about what information they had about the fate of the asylum seekers after they arrived back in Vietnam.

"We don't track people once they've been returned," Major General Bottrell said.

"So how do you know this assurance that there was no retribution has been met?" Senator Hanson-Young asked.

Major General Bottrell said there was no reason not to believe the assurance given by Vietnam.

He agreed with Senator Hanson-Young that the assurance had been taken on "trust".