Abraham Louhenapessy, commonly known as "Captain Bram", helped find a crew and buy a boat for a voyage intended to take 65 migrants to New Zealand in early 2015.
Louhenapessy has long been a notorious figure in the people-smuggling trade.
He is believed to have organised numerous illegal migrant boat voyages from Indonesia, a staging post on long- established routes, with Canberra saying that he has targeted Australia since 1999.
The voyage for which the 56-year-old was convicted today sparked a fierce row between Canberra and Jakarta, due to allegations that Australian officials stopped the boat in their waters and paid its crew about USD 30,000 to turn back to Indonesia.
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"The defendant is sentenced to six years in prison," he said, adding that Louhenapessy also had to pay a fine of 500 million rupiah (USD 37,000) or serve an additional six months in jail.
It was lower than the nine-year term recommended by prosecutors at an earlier hearing.
The people-smuggler has been arrested three times in the past decade, with the most recent occasion being in September.
He was jailed for a brief time after his first arrest in 2007. But when he was detained again in 2009 - after being found holed up on a boat full of asylum seekers - he was only fined.
The boat, carrying Sri Lankan, Bangladeshi and Myanmar migrants, was stopped by the Australian navy as it passed through Australian waters and the passengers and crew were sent back to Indonesia in rickety vessels.
After being detained on Rote, the crew claimed they had been paid to turn back and promise never to engage in people- smuggling again.
The captain and crew were jailed in Indonesia in January last year.
Australia turns migrant boats back to Indonesia when it is safe to do so. The tough policy was introduced to stem the flow of migrants arriving on the country's shores, but it has long been a flashpoint in relations with Jakarta.