Chief navy spokesman Commodore Untung Surapati said Indonesia has beefed up patrols by sending more frigates, fast torpedo craft, corvettes and maritime patrol aircraft to it southern waters.
"All the ships are on the move, patrolling and not merely stationed at a naval base," he told The Jakarta Post.
"We have yet to detect any border violations by the Australians since Friday."
Surapati said he acted on orders from the government's Security Ministry, which criticized Australia for its maritime encroachment and warned Australia to respect its territorial sovereignty, Indonesian news agency Antara reported.
"The Indonesian government has firmly emphasized that territorial violation under any circumstances is a serious threat to relations between the two countries," the ministry's deputy communication director Rear Marshal Agus Barnas said.
"The Indonesian government has a legitimate right to protect and defend its sovereignty and territorial integrity based on international laws and the U.N. charter," he said.
Australia's Prime Minister Tony Abbott went out of his way to issue an "unqualified" apology last week for the incident in an effort to diffuse the latest rift in relations between two countries as they struggle to stop people traffickers.
Australian Immigration Minister Scott Morrison also issued an apology.
"We sincerely regret the incident," Morrison said.
"[We offer] an apology without reserve on behalf of the Australian government because we have not deliberately entered the Indonesian territorial waters."
But Abbott -- who was elected late last year partly on a get-tough asylum policy -- insisted Australia will chase and turn back asylum vessels, the Australian newspaper reported Wednesday.
"Stopping the boats is a matter of sovereignty," Abbott said.
"[Indonesian] President Yudhoyono, of all people, ought to understand -- does understand -- just how seriously countries take their sovereignty."
Australia's relations with Indonesia began heading south in late November after Jakarta suspended military and intelligence cooperation, including joint anti-people smuggling activities, over Australia's alleged spying activities.
Indonesia recalled its envoy after leaked documents indicated Australia tried to spy on senior government politicians, including tapping the cellphones of President Susilo Bambang Yudhoyono and members of his inner circle.
Abbott, immediately upon taking office, set up Operation Sovereign Borders -- an amalgamation of Australia's 12 agencies involved in border protection under the command of a single three-star military commander.
Apart from the issue of over-burdened refugee camps in Australia, and in camps set up in neighboring Nauru and Papua New Guinea, there is increasing concern about the number of deaths from the sinking of the overloaded often unseaworthy vessels.
An investigative report in the Sydney Morning Herald in October found 1,500 asylum seekers have died trying to reach Australia since 1989.
Australia's treatment of asylum seekers also is increasingly being criticized at home and abroad.
The Australian Broadcasting Corp. obtained video footage of asylum-seekers receiving medical treatment in Indonesia for burns they allege were inflicted when the Australian navy towed their boat back to Rote Island within Indonesian waters.
The video shows Indonesian doctors assessing the burns.
Indonesian police reportedly sought medical treatment for seven people with burns on their hands after the navy allegedly forced them to hold on to hot pipes from the boat's engine, ABC reported.
Morrison rejected the asylum seekers' claims, saying it was an attempt to discredit Australia's border protection operations, the Australian reported.
"The government rejects any allegation of inappropriate behavior by our navy or customs and border protection personnel in the conduct of their duties," he said.
Australia's human rights watchdog announced an inquiry into treatment of the estimated 1,000 children that have accompanied asylum-seekers.
"We're not getting the level of information [from the government] we used to get," Australian Human Rights Commission President Gillian Triggs said.