The migrants were about to take the risky ride from Mullaithivu in the island's north east coast to Australia, said naval spokesman Kosala Warnakulasuriya.
This was the first arrest of the illegal migrants to Australia via the sea route for several months.
In 2012, Australia and Sri Lanka launched a joint cooperation programme to curb illegal migration as the number of Sri Lankan asylum seekers increased to alarming levels.
Australia has sent back over 1,400 asylum seekers since August 2012 having placed off shore processing centres in Papua New Guinea and also provided a surveillance boat to the Sri Lankan Navy.
Majority of the asylum seekers allege harassment in Sri Lanka following the war between the Tamil Tigers and the army and want to leave the country, prompting the Australian government to take tough measures to prevent them from reaching that country.
Sri Lankan government, however, says the asylum seekers are moving away because of economic reasons and discourages any Australian attempt to offer them asylum.
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