Under Canberra's hardline measures, asylum-seekers trying to reach Australia by boat are either sent back to where they departed or to remote Pacific island camps, where living conditions have been criticised.
The government has defended the policy as stopping deaths at sea.
Since the start of its "Operation Sovereign Borders" in September 2013, it has managed to halt the flood of boats, and drownings, that characterised previous Labor administrations.
In March, Canberra hailed 600 days with no vessels arriving, with 25 boats carrying 698 people turned back and "safely returned to their country of departure".
"I can advise that there were 12 people on that vessel," he said.
"And the vessel had departed from Sri Lanka and we were able to successfully return those 12 people, which included men, women and children, back safely to Sri Lanka on May 6.
"Now, that brings to three the number of vessels that have sought to arrive and have been turned back, people returned back to their country of origin, in this calendar year."
He gave no details on the other two boats.
The Australian Broadcasting Corporation said that after being spotted, those on board were transferred from a customs ship to a smaller boat, which took them ashore.
They were flown back to Colombo on a charter flight in a secretive operation under the cover of darkness on Thursday, the broadcaster said, citing witnesses who claimed there were seven children, including babies, among them.
Dutton reiterated that no boatpeople, even if found to be genuine refugees, would ever be settled in Australia.
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