Updated

The State Department has confirmed that U.S. troops have captured a senior Pakistani Taliban commander in Afghanistan.

Deputy spokesperson Marie Harf told reporters Friday that U.S. forces nabbed Taliban terrorist leader Latif Mehsud in a recent military operation. Harf said Mehsud served as a senior deputy and trusted confidant of Pakistan Taliban leader Hakimullah Mehsud.

The Islamic extremist group claimed responsibility for the attempted bombing in New York’s Times Square in 2010 and has vowed to attack the U.S. again, according to Harf. She went on to say the group has also attacked U.S. diplomats and “countless” civilians in Pakistan.

The capture could be a significant blow to the Pakistani Taliban, which has waged a decade-long insurgency against Islamabad from sanctuaries along the Afghan border. They have also helped the Afghan Taliban in its war against U.S-led NATO troops in Afghanistan.

Latif Mehsud was arrested by American forces as he was driving along a main highway in eastern Logar province's district of Mohammad Agha, said the Logar governor, Arsallah Jamal. The road links the province with the Afghan capital, Kabul.

The Pakistani Taliban confirmed the capture, but claimed Mehsud was seized by the Afghan army at the Ghulam Khan border crossing in the eastern province of Khost on Oct. 5.

He was returning from a meeting to discuss swapping Afghan prisoners for money, said Pakistani Taliban commanders and intelligence officials, speaking on condition of anonymity because they were not authorized to talk to the media.

The Pakistani intelligence officials said American forces seized Mehsud while he was with the Afghan army, and that they no longer know where he is.

Mehsud, believed to be around 30 years-old, once served as Hakimullah Mehsud's driver but eventually worked his way up the ranks to become a trusted deputy. The two are not related and Mehsud is a common name in the region.

Jamal said Mehsud was in a car with two or three other men when the U.S. military arrested him.

A spokesman for President Hamid Karzai told the Washington Post that a senior Taliban commander was captured in Logar as he was being driven to a facility operated by the intelligence service for questioning. The spokesman, Aimal Faizi, said the commander, who he did not name, was then taken to an American detention facility in Bagram.

There was no immediate comment from Karzai's office on the report.

The detention apparently angered Karzai and may have contributed to a series of emotional outbursts this week alleging that the U.S. and NATO inflicted suffering on the Afghan people and repeatedly violated its sovereignty.

There were reports that talks on a bilateral security agreement, which have been ongoing in the past two weeks, were delayed because of the incident. American and Afghan officials have been meeting in recent days to negotiate the final details of the deal.

Karzai has ruled out signing the U.S-Afghan deal until disagreements over sovereignty issues are resolved. The U.S. wants a deal in October and is reportedly ready to abandon talks and leave Afghanistan at the end of 2014 if one is not quickly reached.

The U.S.-led international coalition plans to withdraw all its troops by the end of 2014, and America and its allies are considering keeping a small residual force in the country to train and assist Afghan security forces and go after the remnants of Al Qaeda.

But almost a year of negotiations on the deal has failed to yield an agreement -- and it's possible the two sides will never produce one.

Without the United States on board, it is unlikely NATO or any of its allies will keep troops in Afghanistan. Germany has already indicated it will not commit the 800 soldiers it has promised.

Karzai has called a tribal meeting of Afghan elders -- known as Loya Jirga -- for next month to discuss the state of the U.S.-Afghan agreement and advise him on what to do.

The Associated Press contributed to this report.