Mullah Baradar, the Taliban's powerful second in command, has been captured in the Pakistani city of Karachi, senior US officials have confirmed.

The detention of Abdul Ghani Baradar is the most significant breakthrough in many years of the US-led hunt for the Taliban's leaders, and comes as Nato forces continue to advance into Taliban-held areas in the southern Afghan province of Helmand.

Baradar was seized in a secret joint operation by Pakistani and US intelligence forces, according to US government officials quoted in the New York Times. Mullah Baradar has been in Pakistani custody for several days, with US and Pakistani intelligence officials both taking part in interrogations, according to the officials. Though Barack Obama has banned US agencies from using forms of torture such as waterboarding, Pakistani questioning techniques are frequently brutal.

US officials later confirmed the report of Baradar's capture to the Associated Press news agency.

Baradar is believed to have been born in the central Afghan province of Oruzgan. He is the most trusted lieutenant of Mullah Mohammed Omar, the supreme leader of the Taliban, and has been ultimately responsible for the execution of the insurgents' military and political strategy since being appointed to the position in 2002. He is, in effect, chairman of the so-called Quetta Shura – the leadership council of the Taliban, named after the south-western Pakistani city near or in which it is thought to be based – and is known to be close to Osama bin Laden.

That his capture appears to have occurred in Karachi underlines the degree to which senior Afghan militants have used Pakistan as a secure base for their operations, but may also signal a very significant change in attitude on the part of the Pakistani army towards the hardline Afghan Islamist militant movement.

The Pakistani security establishment's ambivalent attitude towards the Taliban has been repeatedly cited as a major cause of the problems that have beset the western intervention in Afghanistan since then fall of the Taliban regime in December 2001.

Baradar, reported to be aged between 41 and 48, may have been forced to flee more secure hiding places alongside the Afghan-Pakistani frontier by the repeated and increasingly effective strikes by unmanned drones. Karachi, a metropolis of 14 million people, was where key 9/11 conspirator Ramzi bin al-Shibh was seized in September 2002.

The New York Times said it had learned of Baradar's capture on Thursday but delayed reporting it at the request of White House officials, who told the newspaper making it public would end a hugely successful intelligence-gathering effort. According to the New York Times, officials said the group's leaders had been unaware of Baradar's capture, and if it became public they might become more careful about communicating with each other.