One of the migrants, Yousif Ibrahim from Sudan, said they were handcuffed, called insulting names, and one was beaten with shoes before and during their voyage back to Indonesia, where they arrived Monday.
The 28-year-old also said four people were left with burn marks on their hands when they were forced to hold on to a hot pipe on their boat as punishment for wanting to go to the toilet.
"We asked for water, they didn't want to give us. They called us inhuman words, like illegal refugees, monkeys from Africa," he told AFP.
Another asylum seeker speaking to local media made similar claims. Australian Immigration Minister Scott Morrison refused to comment on the claims but insisted that Australian personnel act with the "highest levels of professionalism".
Ibrahim was among 45 immigrants, mostly from Somalia and Sudan, who set off from Indonesia, a major transit point for would-be refugees, to make the treacherous sea crossing to Australia last month.
But they were picked up on an island in Australian waters by officers from three Australian navy vessels and towed back to Indonesian waters, he said, as part of Canberra's hardline border protection policies.
It was the first reported instance that the Australian navy has turned a boat back without informing Indonesian authorities, and prompted fresh anger in Jakarta at Canberra's policies.
After stopping on the island, the asylum seekers found themselves surrounded by members of the Australian navy, Ibrahim said.
"They told us to go back to the boat, we refused. Then they used violence against us. One tried to run but they beat him with shoes," he said, speaking from a hotel in Kupang, eastern Indonesia, where they are being housed while their cases are processed.
"They have pistols and weapons. We are afraid."
He said the migrants were handcuffed and taken back to the boat. They were released from the cuffs on the boat and then towed for four days towards Indonesia before the Australians left. They arrived on their own in Rote Island, eastern Indonesia, on Monday.
Hidayat, a senior police officer from the Rote Island area who goes by one name, said one migrant had complained he was forced to hold part of a hot engine and had a blister on his hand.
A Somalian migrant Marke Abdulah Ahmad, who was on the boat, also said the asylum seekers were subject to abuse.
"We were tortured and inhumanely treated by the Australian military," he was quoted as saying by Indonesian news website Tempo.
Morrison refused to comment on the reports in line with his conservative government's decision not to discuss "on-water" activities that are part of its hardline policy, known as Operation Sovereign Borders.
But he added: "All personnel involved in border protection operations associated with Operation Sovereign Borders conduct their roles with the highest levels of professionalism, integrity and personal courage in extremely trying and challenging circumstances."
