"Pakistan had delivered a message early July that they will send Umar Patek to Indonesia," National Anti-Terror Agency (BNPT) deputy chief Tito Karnavian told reporters.
Jakarta's foreign and justice ministries are now working to process Patek's deportation, he said.
Indonesian counter-terrorism police have been tracking Patek for years. One of the most wanted Islamic extremists in Southeast Asia, he has a $1 million bounty on his head under the US government's "Rewards for Justice" programme.
Born in 1970, Patek was allegedly the field coordinator for the massive explosions that flattened nightclubs on Bali, killing 202 people, and placed mainly Muslim Indonesia on the front lines of the global battle against Islamic militancy.
Patek is a suspected member of Al-Qaeda-linked Southeast Asian terror network Jemaah Islamiyah (JI), blamed for a series of deadly bombings targeting Christians and Westerners in Indonesia dating back to 1999.
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