There are fears the bombers' executions could spark reprisal attacks
Indonesian security forces are on high alert after the state execution of three Islamic militants for the 2002 Bali bombings that killed 202 people.
There were reports of clashes as hundreds of supporters attended burials in the men's home villages in Java.
Imam Samudra, Amrozi Nurhasyim and Ali Ghufron (Mukhlas) were killed by firing squad at 0015 (1715 GMT on Saturday).
They were found guilty of planning twin attacks on nightclubs at the resort of Kuta, popular with Western tourists.
Security forces are on alert across the country amid fears of reprisal attacks.
Australia, which lost 88 of its citizens in the attacks, has issued a warning against travel to the country. Britain and the US have done likewise.
The BBC's Lucy Williamson, in Cilacap, near the prison, says the executions took place in darkness surrounded by forest and a handful of witnesses.
Prison officials, who said an autopsy had been carried out, and Haji Chozin, the brother of Amrozi and Mukhlas, confirmed the deaths.
After being washed by their families, the bodies of Mukhlas and Amrozi were flown by helicopter to their home village of Tenggulan in East Java for burial.
Samudra's body was flown to Serang in West Java.
Members of radical groups gathered, along with onlookers, in both villages to meet the bodies as they arrived.
A banner saying "welcome martyrs" was on display at the cemetery where the brothers were to be buried, reported Reuters.
There were also reports of clashes in Tenggulan between hundreds of police and supporters who had surged towards the ambulances carrying the bodies.
Foreign journalists were verbally abused as "infidels".
But the deaths will not evoke much sympathy in Indonesia, where most people supported the sentence and believed the executions should have been carried out much sooner, our correspondent says.
Officials had said the three would be shot in early November but no date had been announced in advance.
Supporters and police clash as coffins are carried through Lamongan
Australian Foreign Minister Stephen Smith said it was "not a day that fills us with any joy or with any celebration" and that his thoughts were with the victims' families.
He warned that Australia continued to receive "credible information that terrorists may be planning attacks in Indonesia".
Prime Minister Kevin Rudd said hundreds of lives had been "fundamentally changed by that murder, so it is those lives we think about today".
Victims and family members have also responded to the news.
"They had to pay the ultimate price for what they did," said Peter Hughes, who suffered severe burns in the attacks. "These guys set about mass murder."
Wayan Rasmi, a Balinese woman whose husband's body was never found following the attacks, said the executions would let her put the past behind her.
"I hope there will not be any revenge from their families and supporters," she said.
The bombings were blamed on the militant group Jemaah Islamiah, widely regarded as a regional affiliate of the al-Qaeda network, but several key suspects have never been caught.
None of the executed men had ever expressed remorse for the attacks, only saying they regretted that Muslims had been killed.
They also said they were keen to be "martyrs" for their dream of creating a South-east Asian caliphate.
However, they made several appeals for leniency and also filed an unsuccessful appeal to be executed by beheading rather that face a firing squad.
They said beheading was a more humane and Islamic form of execution and that being shot amounted to torture.
Correspondents say that while executing the men has sent a strong message, it could also put the country's hard-won security at risk if it inspires other extremists to carry out similar acts.