The official did not say when or where Umar Patek was arrested, but according to the Philippines Army, who has also been hunting him, he was seized on Jan. 25 along with a Pakistani associate believed to have been giving him shelter.

The arrest of Patek, who has a $1 million American price on his head, is a major victory in the global fight against Al-Qaeda and — since he was taken alive — could provide very valuable intelligence about regional militant networks and possible future plots.

Indonesia’s top police detective, Lt. General Ito Sumardi, said he only received a report of Patek’s arrest a few days ago and was sending teams to Islamabad to identify him.

Questions remain over how he got to Pakistan, which remains a magnet for foreign militants seeking contact with Al-Qaeda leaders in the country especially in the northwest territories close to the Afghan border.

Sumardi said he was concerned over how Patek was able to travel across international borders to get here.

Patek, 40, is well-known to intelligence agencies across the world and is believed to have served as the deputy field commander of Jemaah Islamiyah, the Indonesian Al-Qaeda affiliate that carried out the Bali nightclub bombings that left 202 people dead, including 88 Australians and seven Americans.

He’s also suspected in at least two other suicide bombings in Jakarta in 2003 and 2009.

Patek spent time in Afghanistan and Pakistan in the 1980s and 1990s with about 300 other Southeast Asian militants and together they formed the nucleus of Jemaah Islamiyah.

Since 2002, however, Indonesia has rounded up or killed many top militants and he was one of the most senior members of the group still on the run.

News of his arrest initially came from intelligence officials in Indonesia and the Philippines on Tuesday. On Wednesday, a Pakistani intelligence official confirmed the capture, but declined to give any further information. All spoke on customary condition of anonymity.

The officer said Patek was currently being questioned by Pakistani agents.

“It is our policy to send them back to their country of origin. We will eventually give him to the Indonesians,” he said.

After the 9/11 attacks, Pakistan is known to have detained a significant number of foreign Al-Qaeda operatives and secretly sent them to the United States, where many were detained in Guantanamo. The CIA, which still cooperates closely with Pakistan intelligence agencies, would presumably like to have access to Patek, but the Pakistani officer said this would happen only with the consent of Indonesia, which too has worked closely with the United States in the past.

One of Patek’s suspected coconspirators in the nightclub bombing, known as Hambali, was arrested in Thailand in 2003 and sent to the United States, where he is now being held in Guantanamo Bay, Cuba.

His detention was a for a long time a source of tension between Washington and Jakarta, which wanted him tried in Indonesia. The country has arrested, tried and convicted hundreds of militants in a widely praised crackdown.

Asked about the arrest of Patek, US Ambassador to Indonesia Scot A. Marciel said “as far as I know this is not a US government operation. We did not arrest him, we do not have custody of this guy, so I’m not sure there is a US government role in this.” Patek fled to the southern Philippines after the Bali bombings, seeking refuge and training with both the Moro Islamic Liberation Front, the largest Muslim separatist group, and later, the Al-Qaeda-linked Abu Sayyaf, security experts have said.

Philippine military spokesman Miguel Jose said Patek’s arrest would be “a big blow to Jemaah Islamiyah and of course the Abu Sayyaf because they have a tactical alliance.” “Many in the region have heaved a sigh of relief that he has been arrested,” he said.

Maj. Gen. Francisco Cruz, of the Philippine armed forces, said “the threat from JI (Jemaah Islamiyah) in Mindanao has diminished because of that.” In March 2010, Patek was believed to be in Sulu province in the far southern Philippines. According to the Jamestown Foundation, a national security policy institute in Washington, Patek was one of the “last senior JI commanders with significant experience” in the original Afghan Al-Qaeda camps and long-standing ties to the international jihadist network and its donors.