Murat Kaya, 28, was sentenced to more than three years' jail on Friday for his part in the 2016 scheme, but will be eligible for parole from Wednesday after already spending more than 1000 days in custody.

He was arrested in terror raids in Melbourne in May 2016, shortly after the arrest of his younger brother Kadir Kaya, associates Paul James Dacre, Antonio Alfio Granata, Shayden Jamil Thorne and ringleader Robert "Musa" Cerantonio.

They were picked up by Australian Federal Police 200km north of Cairns, towing a seven-metre fishing boat they intended to sail from Cape York in what Supreme Court Justice Michael Croucher on Friday predicted would have been a "doomed voyage".

Murat Kaya had originally intended to travel with them, but pulled out and was not part of plans the men had for their wives and children to later join them.

All six pleaded guilty to a charge of engaging in conduct in preparation for incursions into foreign countries for the purpose of engaging in hostile activities, aiming to overthrow the Philippines government.

Prosecutors said the group was involved in an agreement between October 2015 and May 2016 which involved buying the car and fishing boat, stocking it with supplies including travel guides, language books and handmade maps and codes, including green for 'go', white for 'all good' and black for 'arrested'.

Kadir Kaya, Dacre and Granata each received a maximum four-year sentence and will be eligible for parole from May 10.

Murat Kaya was sentenced to a maximum three years and eight months behind bars on Friday for his lesser role in the plot.

Justice Croucher said he believed allowing their release at the earliest possible opportunity would foster rehabilitation and better protect the community in the long-term.

While he wasn't satisfied they had renounced their extremists beliefs, he saw positive signs they no longer held such views. At least two had asked to take part in de-radicalisation programs, though no such scheme is available for prisoners awaiting sentence.

"You are all adults, otherwise decent, but to some extent vulnerable individuals who fell under the influence of Mr Cerantonio," the judge said.

Cerantonio was described by prosecutors as a "charismatic and persuasive" advocate for the forceful or violent application of Islamic law in the Middle East and southern Philippines since at least 2012.

He'll be sentenced after a plea hearing in March.

Thorne, who was arrested in Saudi Arabia on terror charges in 2011 and deported to Australia three years later, will return to court on Monday.

Cerantonio was deported to Australia from the Philippines in 2014, while prosecutors said Murat and Kadir Kaya and Thorne all made failed attempts to leave Australia on one-way tickets in 2015.

Australian Associated Press