ISLAMABAD, Pakistan — Pakistani commandos rescued 42 hostages early Sunday who were held by militants inside the nation’s military headquarters, after gunmen dressed in army fatigues stormed the building in a brazen attack 18 hours earlier, according to the chief army spokesman.

Four militants and three hostages were killed in the operation, the spokesman, Maj. Gen. Athar Abbas, said. He said that the militants, who had taken both soldiers and civilians hostage, had been armed with explosives.

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Faisal Mahmood/Reuters

Soldiers took positions outside the main gate of the Pakistan army headquarters after an attack by armed men in Rawalpindi on Saturday.

A series of loud explosions and gunshots were heard at the headquarters in the garrison city of Rawalpindi at 6 a.m., shortly before the army announced the freeing of the hostages.

The attack was the third by Taliban militants in Pakistan in a week, and it is a singular embarrassment for the Pakistani Army, exposing its vulnerability to the insurgency that is closely linked with Al Qaeda. It came as the military was planning an offensive against the Taliban in South Waziristan, and it was seen as a statement by the militants that they could attack the army first.

In the initial assault on the headquarters, six people, including a brigadier and a colonel, were killed as the militants broke through a checkpoint in a van. The army had reported initially that there were 10 to 15 hostages.

The army said Sunday that commandos captured the last militant who took part in the assault. He was identified by the army as Aqeel, who also used the alias Dr. Ufman.

The Obama administration, which is in the midst of reassessing its strategy for the region, has asked the Pakistani military to step up its efforts against the Taliban.

American military officials said they were astonished that the militants could penetrate the high-security installation to the extent that they did.

One official, speaking anonymously, said the siege represented “a major security lapse.”

Even before ending the standoff, the government vowed to carry out its Waziristan offensive.

“I want to give a message to the Taliban that what we did with you in Swat, we will do the same to you there, too,” Interior Minister Rehman Malik said, referring to the Swat Valley, where the army drove out the Taliban last summer. He identified the militants involved in the assault as Pakistani Taliban.

The militants’ attack began about 11:30 a.m. Saturday, when 8 to 10 gunmen drove up to what was considered a heavily fortified compound. After a 45-minute gunfight, four of the attackers were killed, General Abbas said, and several others fled into the building. Once inside, the militants took hostages.

The attack on the headquarters came after the new leader of the Pakistani Taliban, Hakimullah Mehsud, warned that the army had become the militants’ main target. The army announced two weeks ago that it planned a major offensive in South Waziristan, the Taliban’s stronghold.

Mr. Mehsud said last weekend that the Taliban would not let the planned offensive go unanswered. It was his first news conference since taking over from Baitullah Mehsud, who was killed in a missile attack by an American drone in August.

The assault and other recent attacks could be the start of the escalation Mr. Mehsud warned about, military analysts said.

In one attack, a suicide bomber blew himself up at the headquarters of the United Nations World Food Program in Islamabad on Monday, killing five United Nations workers. That attack seemed designed to intimidate international aid workers and the agency that the Taliban has said should leave Pakistan.

In Peshawar, the capital of North-West Frontier Province, a car bomb killed 48 people in the busiest bazaar at noon on Friday, when it was most crowded. It was one of the most lethal attacks in a city that has become a consistent target of the Taliban.

Security analysts said the militants had cells planted through out Punjab, the most populous province, and had clearly refined assault techniques from its close links with Al Qaeda in Pakistan’s tribal areas.

According to an account from a senior Pakistani military official who was at the scene when the Rawalpindi attack began, there was initial confusion because the attackers were dressed in army fatigues, and security officers could not tell the difference between soldiers and militants, he said. The van they were driving had military plates, allowing them to approach the checkpoints with less suspicion, an American military official said.

The militants were a mixed group, the Pakistani military official said. Some came from the tribal areas, some from Punjab and some from Kashmir. The men made calls on their cellphones demanding release of prisoners from government custody, the official said.

Another witness, Mansoor Ahmed, told the Geo television network that the men in the van were stopped at a gate. “Soon heavy firing started,” he said. “I saw one terrorist falling down. They have also used hand grenades.”

As the siege developed at the headquarters, the chief of the Pakistani military, Gen. Ashfaq Parvez Kayani, was shown on Pakistani television meeting with President Asif Ali Zardari on the contentious issue of a $7.5 billion, five-year American aid package that the army says interferes with Pakistan’s national security.

Pakistani television reported that Mr. Zardari, who has hailed the aid as a major triumph but has come under direct criticism from the army for accepting its conditions, had agreed to take up the army’s objections with the Obama administration.

The aid package, aimed at bolstering civilian infrastructure, is separate from military aid, of which the United States has provided $10 billion since 2001.

The army had been riding high in public opinion after its offensive against Taliban forces in the Swat Valley in the summer pushed militants out of the area. Stepped up security in Islamabad and Peshawar appeared to have quelled militant attacks in the last few months.

And a lull in bombings after Baitullah Mehsud’s death was interpreted by security analysts as a sign that the Taliban were in disarray.

But the new Taliban leader, Hakimullah Mehsud, appeared intent to launch strikes before the army struck in South Waziristan, said a retired senior army officer, Brig. Mehmood Shah.

A commentator on national security and former senior police officer, Arbab Hidayatullah, said Saturday that the attack had occurred because the military had so far failed to “deliver the mother of all battles” in South Waziristan, giving the “terrorists a free hand to deliver themselves.”

Salman Masood and Ismail Khan contributed reporting from Islamabad, and Eric Schmitt from Washington.

www.nytimes.com/2009/10/11/world/asia/11pstan.html