It is the first reported instance in which the new Australian government has turned a boat back without Indonesian cooperation, and could add to recent tensions between Jakarta and Canberra sparked by a spying row.
The boat was carrying 45 immigrants, mostly from Somalia and Sudan, and arrived on Rote Island in eastern Indonesia in the early hours of Monday, Rote Ndao district police chief Hidayat told AFP.
"Based on interviews with the asylum seekers, they had entered Australian waters near (the Australian territory of) Ashmore Reef on January 4 and were intercepted by an Australian naval boat," said Hidayat, who like many Indonesians goes by one name.
"The Australian boat accompanied the vessel and pushed it back to Indonesian waters towards Rote island," Hidayat said, adding the asylum seekers were given life vests and a water pump.
He said he did not know how far the Australian vessel had accompanied the boat and whether it had entered Indonesia's search and rescue zone or its territorial waters.
"Australian authorities didn't alert us that the boat would be pushed back to the island," he added.
However, he denied reports that the boat had run out of fuel and run aground. Earlier reports also said the boat was forced back to Indonesian waters in mid-December, not this week.
In November, Indonesia refused to accept a group of some 60 asylum seekers who were picked up by an Australian vessel south of the main island of Java.
Canberra eventually agreed to take them to the Australian territory of Christmas Island.
Jakarta has been irked by Canberra's hardline Operation Sovereign Borders, which helped propel conservative Prime Minister Tony Abbott to power in September, warning it could breach Indonesian territorial sovereignty.
The policy involves sending asylum seeker boats back to Indonesia, and buying and destroying boats from fisherman to prevent them being used to ferry asylum seekers to Australia.
Australian Immigration Minister Scott Morrison on Tuesday refused to discuss the boat turn-back, in line with his conservative government's policy of not commenting on "on water" operations.
But he insisted: "It is not the policy or practice of the Australian government to violate Indonesian territorial sovereignty. Any suggestion to the contrary is false."
Hundreds of people have died in fatal sinkings in recent years, often after boarding rickety, wooden boats in Indonesia to try and make the treacherous sea crossing to Australia.
Australia has been trying to repair ties with Indonesia since allegations emerged in November that Canberra attempted to tap the phones of President Susilo Bambang Yudhoyono, his wife and inner circle.
Jakarta has frozen cooperation with Canberra in a number of areas due to the row, including on people-smuggling.