Musharraf's allies are losing patience with that argument. During a trip to the region last month, Deputy Secretary of State Richard Armitage publicly called on Pakistan to act more forcefully against the homegrown groups. One foreign diplomat cited reports that fighters from Lashkar-e-Taiba, one of Pakistan's best known banned militant organizations, had traveled to Iraq in recent months to join other foreigners battling U.S. and Iraqi government forces.
"We have received these reports, and we take them very seriously because we do know there were efforts to take some Pakistanis into Iraq," said the senior intelligence official. But the official said it was unclear whether the efforts succeeded.
Police officers sealed off an area in Karachi in June after the attempted assassination of a top Pakistani commander.
The official also asserted that Musharraf had limited room to maneuver against domestic extremists, given the depth of public anger over U.S. policy in the Middle East. "I think the time has come for others to do more for Pakistan than for Pakistan to do more," said the official. "I think our commitment on terrorism is absolutely unparalleled, and it needs to be acknowledged."
On Dec. 25, Musharraf's high-wire act nearly cost him his life when two suicide bombers drove explosives-laden vehicles into his motorcade in the city of Rawalpindi, where he lives, killing 19 people but leaving the president unharmed. One of the bombers was later identified as a member of a breakaway faction of Jaish-e-Mohammed, one of the main militant groups battling Indian forces in Kashmir. The group was founded with the government's blessing in 2000 by Masood Azhar, a radical cleric.
"Jihadists like Masood Azhar were then the natural allies of Musharraf, hence the ultimate freedom to propagate and recruit jihadis under state patronage," said a former army chief of staff who spoke on condition of anonymity. Azhar may now oppose Musharraf, "but there will be a price," the former official said.
Jaish-e-Mohammed has also been linked to the attack on Aziz, the new prime minister. Investigators have identified the prime suspect in the case as Qari Ahsan, who lived in the same southern Punjab town as Azhar and was considered one of his top lieutenants, intelligence officials said. Azhar has disappeared from view; a senior intelligence official described him as a fugitive.
But the official said it would be a mistake to conclude that Jaish-e-Mohammed and other such organizations had actively turned against the government. "The leadership was under pressure from the government, so you find everyone splintering into small cells acting on their own," he explained.
The official also asserted that as a consequence of Pakistan's counterterrorism efforts, including a series of army operations in South Waziristan this year, the ability of al Qaeda -- and especially its senior leaders, Osama bin Laden and Ayman Zawahri -- to direct attacks had been "very severely curtailed."
At the same time, the official said, "there is probably a second or third tier that has started asserting itself operationally."
A leading example is a Libyan citizen, Abu Faraj Libbi, whom Pakistani authorities accuse of coordinating the December attempts on Musharraf's life. The senior official said it was "quite likely" that Libbi also had a hand in the attempt on Aziz, whose driver was killed in the bombing, although other investigators described the connection as speculative. The official said that Libbi was believed to be directing terrorist operations both in Pakistan and elsewhere from a hideout in South Waziristan.
Pakistani newspapers have run ads offering rewards of up to $345,000 each for information leading to the capture of Libbi and five Pakistanis, including Ahsan, the former Jaish-e-Mohammed lieutenant sought in connection with last month's attempt on Aziz.
The June attack on Hayat, who commands one of Pakistan's nine army corps, has been blamed on a previously unknown group called Jundullah. Its alleged leader, Ataur Rehman, holds a master's degree in statistics from Karachi University and fought with the Taliban when it enjoyed the backing of Pakistan's government during the Afghan civil war of the 1990s, investigators said.
Although officials have not specifically linked that episode to the Libyan, they said that two of the gunmen had admitted spending four weeks under al Qaeda's tutelage at a mud-walled compound in the Shakai Valley of South Waziristan. The compound was one of several destroyed in a major military assault in May.
Khan reported from Karachi.