Australian Prime Minister John Howard described the deployment of the two amphibious transport ships as precautionary and insisted East Timor had not requested any military help.
"We have had absolutely no requests," Mr Howard told reporters before leaving for an official visit to the United States.
"It's what the military does, uses its assets in such a way that if they were to receive any requests we would be able to respond quickly," he said.
East Timor lies about 450 kilometres northwest of Australia.
Foreign Minister Alexander Downer warned this week that the situation remained unstable in East Timor, Asia's poorest country, which has struggled to rebuild since its independence in 2002.
The capital Dili was rocked by a riot on April 28 in which at least five people were killed and more than 100 buildings destroyed or damaged in the worst unrest to hit the nation since it voted for independence from Indonesian rule in 1999.
The trouble began with a rally in support of nearly 600 soldiers from the west of the country who were sacked when they deserted their barracks complaining of ethnic discrimination at the hands of easterners.
While the government played down the violence and has subsequently entered into talks with the disgruntled soldiers, Prime Minister Mari Alkatiri this week accused his political opponents of using the unrest to destabilise his administration.
Foreign Minister Jose Ramos-Horta on Wednesday linked the recent violence to an opposition political party ahead of national elections scheduled for next year.
A number of foreign governments have withdrawn non-essential embassy staff from Dili in the wake of the unrest, which saw up to 20,000 residents flee the capital.
Portugal, the former colonial power in East Timor, said this week that it had drawn up contingency plans to fly its nationals out of the country.
Mr Downer's office has issued travel warnings recommending Australians avoid unnecessary travel to East Timor, but has stopped short of advising nationals to leave the country.
A UN "peace-building" mission in East Timor, UNOTIL, which includes Australian military and police advisers, is due to end next week.
But the UN has said it could extend the group's mandate in light of the unrest.
Mr Downer has backed an expansion of UNOTIL, which replaced an Australian-led military peacekeeping force deployed in East Timor in 1999, to halt violence by pro-Indonesia militia trying to disrupt the territory's move to independence.
Horta meets police
East Timor's foreign minister Jose Ramos-Horta has met with military police who fleed Dili in the wake of last month’s riot.
He travelled to Aileu, 25 kms south of Dili, to where 20 military police and four members of the military's Rapid Intervention Unit stationed themselves after the riot.
"The conversation was conducted in a most fraternal and honest atmosphere with the soldiers pledging their allegiance to the head of state and to F-FDTL (the military)," Mr Ramos-Horta's office said in a statement.
The men, who took their weapons with them, said they had not deserted and "expressed their strong opposition to violence and pledged they will not be involved in any actions that would harm anyone including the government."