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ISLAMABAD — Even as it revealed growing skepticism toward Pakistan’s powerful military, an extraordinary national security conference ended here late Thursday with a statement rejecting as “baseless” allegations from America’s top military official that Pakistan was facilitating militant attacks in Afghanistan.

Military leaders and more than 50 politicians representing 32 political parties gathered at the residence of Prime Minister Yusuf Raza Gilani to discuss the charges made by Adm. Mike Mullen, chairman of the Joint Chiefs of Staff. Last week, Mullen told a Senate panel that the Haqqani network, a potent part of the insurgency battling U.S. forces in Afghanistan, was a “veritable arm” of Pakistan’s spy agency. He also accused the agency of supporting an attack this month by Haqqani militants on the U.S. Embassy in Kabul, the Afghan capital.

The statements reopened a rift between the nominal allies and set off a furor in both countries, with the White House on Wednesday seeking to temper the remarks. In an interview with National Public Radio on Thursday, however, Mullen stood by his testimony, revealing a divide within the Obama administration that has, unusually, placed Mullen publicly in the hard-line position toward Pakistan. He has been the U.S. official leading the effort to improve cooperation.

He would not change a word of his testimony, Mullen insisted, saying, “I phrased it the way I wanted it to be phrased.”

Since his remarks last week, an atmosphere of crisis has gripped Pakistan, and the meeting Thursday was called to address fevered speculation among politicians and in the media that the United States was preparing to attack Haqqani havens, which U.S. officials have said are in North Waziristan, a part of Pakistan’s tribal areas bordering Afghanistan.

On Thursday, Pakistani politicians issued a 13-point resolution saying that Mullen’s “assertions are without substance and derogatory to partnership approach.” They extended full support to the country’s armed forces “in defeating any threat to national security.”

The meeting of top officials here was addressed by Gilani and Foreign Minister Hina Rabbani Khar. The Pakistani army chief, Gen. Ashfaq Parvez Kayani, and chairman of the Joint Chiefs of Staff Committee, Gen. Khalid Shameem Wynne, also attended the meeting, which lasted more than seven hours.

Most notable was a briefing by Lt. Gen Ahmad Shuja Pasha, director general of the spy agency, the Inter-Services Intelligence Directorate, or ISI.

According to various accounts provided afterward by participants and local news networks, which cited unnamed sources, Pasha said that though Pakistan “did not want to take relations with the United States to the point of no return, it also was capable to defending itself in case of an attack.”

“Any U.S. attack against Pakistan in the name of extremists would be unacceptable,” he said.