The attorney general’s office said the court had cleared Bashir of taking part in a plot to overthrow the government but upheld his conviction for immigration offences and forging documents.
“The copy of the High Court’s decision that we just received says the charge of treason was not proven,” said office spokesman Kiemas Yahya Rachman.
The decision was dated November 10. Appeal court rulings are not made public when they are delivered.
The latest ruling was likely to further dismay foreign governments, who insist that the elderly cleric headed the al Qaeda-linked Jemaah Islamiyah (JI) terror group.
Bashir, 65, denies any links to terrorism and says he was framed by Washington because he campaigns for Sharia.
Analyst Sidney Jones, an expert on JI, called the ruling a setback in efforts to counter terrorism. However Bashir’s lawyer Ahmad Michdan said he would appeal to the Supreme Court to have all charges dropped.
In September, after a months-long trial, a district court convicted Bashir of taking part in a JI plot to overthrow the government. But it said prosecutors had not proved that Bashir heads the network.
The court jailed him for four years rather than the 15 years which prosecutors had sought.
Australia, which lost 88 citizens in the Bali bombings blamed on JI, expressed disappointment at the time that Bashir had not been convicted of leading JI and had not received a heavier sentence.
JI is blamed for a string of bloody attacks including church bombings which killed 19 people on Christmas Eve 2000, the Bali blasts on October 12 last year that killed 202 people and the Marriott hotel blast in Jakarta that claimed 12 lives in August.—AFP