The two boats were caught near Saumarez reef in a joint Australian Border Force (ABF) and Australian Fisheries Management Authority (AFMA) operation, and are being escorted to Gladstone in Queensland.
AFMA said 13 tonnes of bêche-de-mer (sea cucumber) was found on board. The 29 crew are being investigated for breaches of the Australian fisheries and environmental laws.
Increasing numbers of the so-called 'blue boats' are illegally fishing in South Pacific waters, appearing in Papua New Guinea, New Caledonia, Palau, Micronesia and in northern Australia.
In 2016, 10 Vietnamese boats were detained in Australian waters, with 121 of 146 fishermen convicted and 32,000 tonnes of bêche-de-mer seized.
Boats have been sighted for the first time in Vanuatu this year and at the end of January two of three boats detained in New Caledonia escaped, reportedly headed for Australian waters.
AFMA confirmed the ones intercepted on 17 February are not those wanted by New Caledonian authorities.
"Surveillance is carried out in co-operation with Australia, with which there is a common border between the two exclusive economic zones (EEZ)," French national broadcaster in New Caledonia NC 1ère reported in early February, saying Australia had not reported any sightings.
A surveillance plane from Maritime Boarder Command, a taskforce within Border Force, first spotted the two boats on February 15 and the HMAS Bathurst boarded them at sea.
"Foreign fishers seeking to take advantage and target our fish resources will be caught and run the risk of being prosecuted and having their boats confiscated and destroyed," AFMA's general manager of operations Peter Venslovas said.
Last year eight 'blue boats' were destroyed in Cairns and Gladstone, and two caught fire at sea and sank.