"Umar Patek was arrested in Pakistan," the official told AFP on condition of anonymity, without giving further details about where or how Tuesday's arrest was made.
There has been no immediate confirmation from authorities in Pakistan.
Indonesia's counter-terrorism police have been tracking Patek for years. He has a $1.0 million bounty on his head under the US government's "Rewards for Justice" programme.
Born in 1970, he was the alleged field coordinator for the 2002 bombings of nightclubs in the Indonesian resort island of Bali, which killed 202 people including Australians and Americans.
Patek is a suspected member of Jemaah Islamiyah, an al Qaeda-linked militant group active in Southeast Asia, and Indonesian authorities believe that he has been hiding out in the Philippines.
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