Muhammad Cholili, 36, was sentenced to 18 years in prison in September 2006 for assisting slain ringleaders Noordin Mohammad Top and Azahari Husin to assemble the explosives used in the blasts.
The attacks on restaurants on October 1, 2005 left 20 people dead and over 100 injured.
Noordin and Azahari were key members of the Al-Qaeda linked Jemaah Islamiyah extremist network blamed for a string of deadly attacks in Indonesia, including the 2002 Bali bombing which killed 202 people, mostly Western holidaymakers.
Sentences are routinely cut in Indonesia to mark major religious celebrations such as Eid al-Fitr Muslim holiday and the country's independence day on August 17.
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This meant that Cholili served only around half of his term, but Yusanti said that his release has "received the recommendation from the Detachment 88 and the National Anti-Terror Agency," which are responsible for tracking terror activities in the country.
Yusanti also added that the authorities would continue to monitor Cholili's activities and he will not be able to leave Indonesia without the justice minister's approval.
Indonesia's English daily The Jakarta Globe reported that Cholili was surprised to learn of his release from the Lowokwaru Prison in Malang, East Java, but was happy to leave prison.
"The most important thing is to go home and meet my family," he was quoted as saying by the newspaper.
Indonesia, the world's biggest Muslim-majority nation, has long struggled with terrorism but a successful clampdown in recent years has prevented major deadly attacks.
However, recent reports of Indonesians joining the procession of jihadists to Syria and Iraq have sparked fears that they will revive sophisticated militant networks.