Prosecutors have said they will appeal the four-year sentence given to Indonesian Muslim cleric Abu Bakar Ba'asyir for subversion, which has been criticised in the West as too lenient.
Ba'asyir has also said he will appeal his sentence
Antasari Azhar, spokesman for the Attorney General's office, said the appeal would focus on the primary charge that Ba'asyir led the regional militant group Jemaah Islamiah, a charge he was acquitted of at his trial last week.
"We can't accept (the verdict) because we think the charges
were proven in court," Mr Azhar told Reuters news agency.
Prosecutors had called for a 15-year sentence for Ba'asyir.
The move came as the cleric described top Asian terror suspect Hambali, who is suspected as acting as operations chief for JI, as a "good man".
Hambali is in US custody at a secret location following his arrest in central Thailand last month.
Ba'asyir's lawyers have also said they will appeal against their client's sentence. The cleric has repeatedly denied any wrong-doing, and has insisted he has never even heard of JI, which has been widely blamed for last year's Bali bombings.
The judges in his case ruled that although there was no evidence to support the claim that Mr Ba'asyir founded JI, they said that he clearly knew of the group and supported its aims.
The case has been widely regarded as a litmus test of Indonesia's commitment to combat radical Islam.
Hasyim Muzadi, head of the largest Muslim group in Indonesia, Nahdlatul Ulama, was quoted in the Jakarta Post as saying that the verdict "is proof that JI does not exist in Indonesia even if it exists in other countries".
The US authorities will hope that Hambali's interrogators can shed more light on JI, and its reach.
He is believed to have financed the Bali attack, and to act as Osama Bin Laden's point man in South East Asia.
But Ba'asyir told Monday's Koran Tempo newspaper that "Hambali is a good man. I know that."
"I am not convinced that Hambali was aiming at doing an act of terror... Hambali's aim is to defend Islam and fight America but he just went over the limits," Ba'asyir said.
"I am certain that if he did conduct the bombings, something must have been wrong," the cleric was quoted as saying.