Attending a ceremony in Colombo harbour, Scott Morrison said the claims by some of the 41 returned asylum-seekers were offensive.
"I find those allegations offensive and reject them absolutely," Morrison told reporters after the ceremony with President Mahinda Rajapakse to commission two boats donated by Australia to combat people-smuggling.
He dismissed rights groups' concerns that the migrants could be mistreated after being sent back to Sri Lanka. "We don't have those concerns, based on the assurances (from Colombo) to the previous (Australian) government," he said.
Some claimed they were racially abused, denied medication and given out of date food by customs officers. Several said they had been trying to get to New Zealand to find jobs.
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The group appeared in a court in the town of Galle yesterday charged with illegally leaving the country, after spending the night in a Sri Lankan high-security detention centre upon their return.
While the children were discharged, the rest of the group face an initial charge of breaking immigration law, which carries a maximum penalty of two years in jail.
Australia has come under fire over the transfer, with experts saying its shipboard screening to determine whether the migrants had refugee status appeared inadequate under international law.
Morrison declined comment on the fate of another 153 Sri Lankans being held in custody on the high seas, saying the matter was still before the courts.
Australia faces growing pressure over its immigration policies with High Court action under way over the 153, who are currently detained on a customs boat.