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In Washington, officials are crowing about the capture of the Taliban's top military commander several days ago during a secret raid by CIA and Pakistani intelligence agents in the port city of Karachi. After all, Mullah Abdul Ghani Baradar is described as the Taliban's second in command after the movement's spiritual leader, Mullah Mohammad Omar. But in Islamabad, the official line was denial. Interior Minister Rehman Malik told the media, "We don't do joint raids [on our own territory with the Americans]. We are a sovereign state." It is a prudent stance for the Pakistani government to take, what with anti-Americanism running high after recent U.S. drone-missile strikes in the tribal areas.

Nevertheless, a few Pakistani intelligence officials, who refuse to be quoted or named, admit that Baradar has been captured, a staggering blow to the Taliban leadership at a time when its stronghold of Marjah, in southern Afghanistan, is besieged by a U.S.-led ground and air assault. "If it's confirmed, this will be a real setback for the Taliban," says Rahimullah Yusufzai, a Peshawar journalist who has long tracked the activities of the Taliban. According to the New York Times, which first broke the news of Baradar's arrest on Monday, both Pakistani and American intelligence agents were taking part in his interrogation, presumably somewhere in Pakistan.

The commander's arrest would mark a significant departure from Pakistan's policy toward the Taliban. Usually, Islamabad officials deny to the Americans that they know where the top commanders are hiding while letting them move freely among the Pakistani cities of Quetta, Peshawar and Karachi as well as the country's tribal areas, where the jihadi fighters launch their attacks and suicide bombings against U.S.-led forces inside neighboring Afghanistan. Pakistani officials privately say they regard the Taliban in Afghanistan as a strategic asset in their regional rivalry with India, which supports President Hamid Karzai in Kabul.

Some Taliban contacts suggest that Pakistan may have had no option but to cooperate this time, since the CIA may have tracked down Baradar in Karachi on its own and pressured Pakistani spy agency the Directorate for Inter-Services Intelligence (ISI) to help pick him up. A senior Pakistani official told TIME that the CIA "pinpointed the general area" and that Pakistani intelligence on the ground made the arrest in the night between Feb. 10 and 11. Baradar was arrested in the slum town of Baldia, just outside Karachi, which is teeming with migrant Afghans and Pashtuns. The Pakistani official insisted that "this shows that Washington and Islamabad's priorities are starting to match up." U.S. officials have complained that past efforts to tip off the ISI to the locations of Taliban commanders yielded no action. Until Baradar was seized, no significant Taliban fighter had been arrested in two years in Pakistan. "All of the major Taliban commanders are in Pakistan," a source close to the Taliban told TIME — an allegation that Islamabad loudly and persistently denies.

In Karachi, an anarchic city of 15.5 million people with more than 2,000 mosques, the Taliban can easily hide. After President Barack Obama wrote a stern letter several months back to the Pakistanis threatening to expand the use of the missile-armed drones into Baluchistan and its provincial capital of Quetta, top Taliban commanders — Baradar among them — supposedly fled to Karachi. There, in the warren of the city's slums, surrounded by millions of their fellow Pashtun tribesmen, the Taliban have reportedly found a safe haven. For years, Karachi has been, as a political analyst in Islamabad put it, "an R&R place" for the Taliban, where they can hide and also raise funds and recruit eager youths from the madrasahs, or religious schools, for jihad. Karachi also served as a hideout for several top al-Qaeda fugitives, including Khalid Sheikh Mohammed, the alleged mastermind of the 9/11 attacks.

Pakistani sources close to the Taliban tell TIME that Baradar, a veteran from the jihad against the Soviets in the 1980s, was next only to Mullah Omar in authority and had been at his side as a friend, trusted adviser and skilled military commander since the movement was formed in 1994 in a poor religious school outside Kandahar. Since 9/11, say these sources, Baradar had been the link between Omar and the shadowy military council known as the shura, which has been leading the Taliban's bloody campaign against NATO forces in Afghanistan. Baradar's capture may bring U.S. and Pakistani authorities a step closer to finding the elusive Omar, who along with Osama bin Laden was the main target of the U.S. invasion eight years ago.

As head of the Quetta shura — named after the southwestern city where until recently U.S. and Afghan officials believed the top Taliban commanders were hiding — Baradar was in charge of planning the campaign against NATO troops, allotting funds and weapons and picking commanders to set up a shadow administration of militias and courts that today hold sway over much of the Afghan countryside beyond NATO's limited reach.

Even if Baradar cannot be persuaded to reveal where Omar and the other commanders are hiding, he may prove valuable in other ways. Pakistani and Afghan officials have lately been saying that the Taliban can never be defeated militarily and that a peace deal could be struck only with the Taliban leadership. It is a notion that the Obama Administration has thus far been resisting. Washington wants to limit "reconciliation" to only mid-level Taliban fighters and below, excluding Omar and the military shura. In captivity, Baradar could prove to be a bargaining chip in any future peace talks between Washington and the Taliban leaders still at large.

• Tim McGirk and Omar Waraich / Islamabad
• The Pakistanis deny that there was a joint operation to arrest Mullah Abdul Ghani Baradar. But they might have have had no choice