Umar Patek, who faces the death penalty if convicted, told judges his role was minor and that he didn't plant the bombs that killed more than 200 people.
The bombs, which were planted in Paddy's Bar and the Sari Club, exploded with devastating effect. The dead were from 21 countries, including 88 Australians, 38 Indonesians and 28 Britons.
Patek told judges at the West Jakarta District Court that he didn't want the bombs to be detonated in Bali and tried to reason with the people making the bombs, a report in the Jakarta Globe said.
"I was very sad and regret that the incident happened," Patek said. "I was against it from the start, I never agreed with their methods," said Patek who appeared in white clothes and sporting a small beard.
Patek, 45, said he believed the Bali bombers were motivated by the Palestinian conflict but didn't know how to get to Palestine to wage jihad there, the Globe reported.
"They wanted to bomb a place with a lot of Westerners in retaliation for the killing of Muslims in Palestine," he said.
"I asked 'why Bali? Jihad should be carried out in Palestine instead.' But they said they didn't know how to get to Palestine. Dulmatin told me not to think so hard, just to help."
Dulmatin, killed by police during a raid in March 2010, was a senior member of the terrorist group Jemahh Islamiyah, which allegedly has links to al-Qaida.
Patek said he had ''no idea'' in which Bali bars the bombs were going to be planted but knew the people making the bombs were looking for places frequented by many foreigners, a report by the BBC said.
"I am taking this opportunity to seek forgiveness from the victims, their families and whoever suffered losses," he said.
Patek also said he lived in the Philippines from 2000 to 2002 and fought with the Moro National Liberation Front, a local terrorist organization operating in the southern Mindanao Island.
He said he visited Abu Bakar Asy-Syidiq's training camp and helped fight off an attack by the Philippine army.
"Around May and July of 2000, there was this huge battle at Abu Bakar Asy-Syidiq's military camp," Patek recalled. "The Philippine military tried to take over the camp. I was there, joining the fight."
Patek was arrested in January 2011 in the Pakistani garrison town of Abbottabad -- where Osama bin Laden was later killed in a U.S. raid -- and extradited to Indonesia.
Last week an American survivor of the bombing at Paddy's Bar told the court there was total confusion immediately after the blast, a report in the Jakarta Post said.
"Inside the bar was like being in the eye of a hurricane," Cabler said. "I have no compassion for the people who committed this crime. I love this country and have much respect for the people and the culture."
Cabler was with a friend of 25 years celebrating his birthday when the bomb went off.
"My friend John was between me and the explosion ... when the explosion happened, it was big, it was massive, I hit my head very hard against my friend's head ... and my eardrums exploded."
His friend, Stephen Webster, was among the dead.
Patek's trial began in February and is expected to end June 21.