The three countries aren't believed to be among the 10 unnamed countries in the government's counter-terrorism white paper. The long-awaited document outlined plans to, among other things, detect terrorists traveling to Australia.
It sets out a controversial $61 million fingerprint and facial data program for people seeking visas to visit Australia.
Initial media reports quoted unofficial sources as saying that, apart from India, Pakistan and Indonesia, the list of countries to which the program will apply includes Somalia and Yemen.
Critics are saying the tougher visa application program could have complicated already delicate relations with India whose Tourism Minister Kumari Selja canceled a visit to Australia last June.
A report by the BBC at the time said she put off the July visit because of the "prevailing atmosphere" in Australia. Indians in Australia had suffered several attacks that the government denied were race-based. Australian police called the crimes "opportunistic" and Indian students were seen as "soft targets."
There is no confirmation by the Labor government of Prime Minister Kevin Rudd of which countries are on the so-called visa black list. But The Australian newspaper said it has learned that the three countries are not on it.
This is despite those countries being the sites to a number of terror attacks, The Australian's report said. Indonesia, the world's most populous Muslim nation, is the site of more Australian deaths at the hands of terrorists than any other country.
Yemen and Somalia, identified in the paper as the emerging centers of radical Islamic terrorism, will be included.
But the white paper fingers home-grown extremists -- as opposed to groups such as al-Qaida that are mainly based overseas -- as the main terror threat confronting Australia.
The prime minister warned the threat from terrorism was now "permanent" and "persistent" and could happen at any time, he told reporters in Canberra at the release of the document.
"Prior to the rise of jihadist terrorism, Australia was not a specific target. Now Australia is," said Rudd who noted there had been some success with counter-terrorism efforts in other countries, including Afghanistan and Pakistan.
The government wants to build on these existing counter-terrorist agreements with other countries in Asia, including the Philippines, Malaysia, Cambodia, Thailand, Brunei, East Timor and Bangladesh.
The 83-page "Securing Australia, Protecting our Community," accessible on the Web site of the Department of the Prime Minister and Cabinet, singles out the South Asia-wide group Jemaah Islamiyah and its offshoots such as the Abu Sayyaf group. This is "the most prominent terrorist group in South East Asia since the late 1990s" with its roots in Indonesia, the white paper states.
Jemaah Islamiyah is held responsible for major anti-Western attacks affecting Australians. "Since 2001, more than 100 Australians have been killed in terrorist attacks overseas," the document noted.
These include the October 2002 Bali nightclub bomb that killed 202 people, 88 of whom were Australians; the September 2004 bombing of the Australian Embassy in Jakarta, which killed 10 people; and the July 2009 bomb in the bombing of Jakarta's Marriott and Ritz Carlton hotels that killed three Australians.
The white paper said that in Australia "38 people have been prosecuted or are being prosecuted as a result of counter-terrorism operations" and 20 people have been convicted of terrorist acts. Also, more than 40 Australians had passports revoked or passport applications denied "for reasons related to terrorism."
The recently announced Counter-Terrorism Control Center, within the Australian Security Intelligence Organization, will be the focus of anti-terrorist activity. The document also promises to ensure intelligence is shared among such organizations through the National Intelligence Coordination Committee which is led by the government's national security adviser.
Apart from the recently announced $178 million investment in aviation and border security operations, including body scanners at airports, the government will start the four-year, $61 million investment in "a bio-metric based visa system for certain non-citizens."
This will mean gathering fingerprints and facial data from potential visitors, a controversial move according to some media reports. Foreign Minister Stephen Smith acknowledged that "there may well be a diplomatic effort required in respect of some of those countries as you would expect."