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“Even if Pakistani diplomats have been sincere, the fact of the matter is that the ISI seems to have been running the show and the diplomats were quite irrelevant.”

But a spokeswoman for Pakistan’s ministry of foreign affairs said Pakistan has played a significant role in efforts to eliminate terrorism and described intelligence sharing with the U.S. as extremely effective.

Critics have long accused elements in Pakistan of supporting terrorist groups, including al Qaeda, the Pakistani Taliban, the Haqqani Network and Lashkar-e-Toiba.

“Elements within the ISI certainly continue to maintain ties with the Haqqani Network who continue to enjoy ‘most favored’ status among Pakistan’s Afghan proxy groups,” said Jeffrey Dressler, a research analyst at the Institute for the Study of War.

The Haqqani Network is led by a father-son duo, Jalaluddin and Sirajuddin Haqqani.

“Al Qaeda’s relationship with the Haqqanis certainly raises questions about how much elements within the Pakistani security establishment may or may not know about the current status of al Qaeda in Pakistan,” Mr. Dressler said.

The U.S. did not inform Pakistani authorities of the mission until after it was concluded, prompting accusations from some Pakistanis of a violation of sovereignty.

Pervez Musharraf, Pakistan’s former president, told CNN-IBN, an Indian news channel, that U.S. troops operating in Pakistan is “not acceptable to the people of Pakistan. It is a violation of our sovereignty.”

A U.S. official said that since the Sept. 11, 2001, terrorist attacks, the United States has made it clear to Pakistan that it would pursue bin Laden wherever he might be.

Meanwhile, Taliban spokesman Ahsanullah Ahsan claimed that the terrorist group will “avenge the martyrdom of Osama bin Laden, and we will do it by carrying out attacks in Pakistan and America.”

The U.S. closed its embassy in Islamabad and its consulates in the cities of Lahore, Karachi and Peshawar on Monday as a precautionary measure.

This article is based in part on wire service reports.