Patek, a member of the Jemaah Islamiyah terror network, was captured by the ISI recently, an unnamed officer of the spy agency told The News daily.
"We captured him a few days ago and now as is the protocol, the Ministry of Interior, Ministry of Foreign Affairs and other related departments will ensure that he is taken back to Indonesia," the officer said.
The arrest of Patek, who has a USD 1 million price tag on his head announced by America, ends a 10-year international manhunt.
35-year-old Patek, an Indonesian of Javanese and Arab descent, is being interrogated by the ISI and will be handed over to Indonesia only after his questioning is completed, the report said.
Asked if Patek was arrested due to a joint effort by several intelligence organisations, the ISI officer replied: "No, it was entirely the efforts of the ISI."
The officer refused to reveal more details, including the place of Patek`s capture, or to say what the alleged terrorist was doing in Pakistan as the Jemaah Islamiyah is not known to have carried out any terrorist activity in the country.
The officer hinted that Patek might have come to Pakistan thinking it was a "safe haven".
The Foreign Office spokesperson said it had not received any information from the ISI so far.
Western media reports have said the ISI arrested Patek after receiving a tip-off from the America`s Central Intelligence Agency.
Details about what he was doing in Pakistan remain murky, raising questions about whether he was here to plan an attack with al-Qaeda`s top operational leaders.
Patek, wanted in Indonesia, the Philippines, Australia and the US, is believed to have served as a field commander in the 2002 nightclub bombings that left 202 people dead, many of them foreigners.
He is also believed to have been among a group of Indonesians, Malaysians and Filipinos who travelled to Afghanistan and Pakistan during the 1980s and 1990s for training at terror camps.
Indonesian police have sent a team to Pakistan to confirm that the arrested suspect is Patek.
Indonesian authorities are also coordinating with Interpol to confirm Patek`s identity.