Agus R. Barnas, spokesman for Indonesia's Ministry of Legal, Political and Security Affairs, said Friday his country "has a legitimate right to protect and defend its sovereignty and territorial integrity" in accordance with international law and the U.N. charter, the New York Times reported.
Australian Prime Minister Tony Abbott implemented a controversial policy in September to stop thousands of people from using Indonesia as a transit hub to board boats bound for Australia to seek asylum. The policy includes a provision allowing Australian authorities to force the boats back into Indonesian waters.
The Sydney Morning Herald reported three navy ships and one Customs ship crossed the 12-nautical-mile limit on five occasions since Dec. 13.
Earlier Friday, Australian Immigration Minister Scott Morrison said in Canberra at least one border protection boat earlier this week "inadvertently entered Indonesian territorial waters on several occasions in breach of Australian government policy."
Australia offered an "unqualified apology" to Indonesia, Morrison said.
Relations between the two countries have been tense as a result of documents leaked by Edward J. Snowden, the former U.S. National Security Agency contractor, said the Australian Embassy in Jakarta was part of a U.S.-led spying effort in Asia. The documents also said Australian officials tried to bug the phone of Indonesian President Susilo Bambang Yudhoyono.
In response, Yudhoyono's government halted cooperation with Australia on stopping asylum seekers' boats.
Agus said Friday the Indonesian Navy would station a frigate in Kupang as part of the country's increased security patrols. He told the Times the move wasn't a challenge to Australia but show Indonesia's commitment to staunching the flow of asylum-seekers.
A source told the Morning Herald a review announced Friday by Morrison would help clarify whether border protection authorities were "playing too fine a line in positioning the ships too close to Indonesian waters."