Abu Bakar Bashir was thought to be a key figure in regional terror network Jemaah Islamiyah, blamed for the 2002 Bali bombings that killed more than 200 people, mostly foreign tourists.
The elderly, bespectacled preacher was sentenced to 15 years in jail in 2011 for helping fund a paramilitary group training in the staunchly Islamic province of Aceh, which allegedly planned to kill the then president as well as Westerners.
The 77-year-old was jailed after authorities in the world's most populous Muslim-majority country broke up the camp.
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He launched a challenge against his conviction in January, with hundreds of chanting supporters staging a rally as he made a rare appearance in court at the start of the appeal.
The cleric's legal team had argued that funds he collected were intended to help people in the Palestinian territories, but ended up getting sent to the Aceh group without his knowledge.
However the Supreme Court said on Thursday it had rejected the appeal "because of a lack of new evidence".
"That means he will stay in prison," said court spokesman Suhadi, who like many Indonesians goes by one name. Bashir's lawyer Mahendradatta pledged to find new evidence and continue fighting the conviction.
The Supreme Court handed down the ruling last week. The court holds hearings behind closed doors and typically takes some time to announce decisions.
Bashir was also previously handed a jail sentence over the Bali bombings but that conviction was quashed on appeal.
Indonesia was hit by several militant attacks between 2000 and 2009 but a crackdown weakened the most dangerous networks.
But the Islamic State (IS) group has proved a potent new rallying cry for the country's radicals, with hundreds travelling to the Middle East to join the extremists. A deadly gun and bomb attack in Jakarta in January was claimed by IS.
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