The US has confirmed that American troops are holding a senior Pakistani Taliban commander.
The detention is a blow to the Pakistani Taliban who have waged a decade-long insurgency against Islamabad and were responsible for the failed 2010 attempt to detonate a bomb in New York's Times Square.
"Mehsud is a senior commander in TTP, and served as a trusted confident of the group's leader, Hakimullah Mehsud," Ms Harf said. "TTP claimed responsibility, as folks probably know, for the attempted bombing of Times Square in 2010 and has vowed to attack the US homeland again. TPP is also responsible for attacking our diplomats in Pakistan and attacks that have killed countless Pakistani civilians."
The news surfaced as Secretary of State John Kerry was in Kabul trying to negotiate the terms of a US-Afghan security agreement that would govern the activities of American forces in Afghanistan after the Nato-led combat mission ends at the close of next year.
Ms Harf said she did not have any details of how, when or where Mehsud was captured.
Arsallah Jamal, governor of Logar province in eastern Afghanistan, said Mehsud was captured a week ago as he was driving along a main highway in Mohammad Agha district. The road links the province with the Afghan capital, Kabul. Mr Jamal said Mehsud was in a car with two or three other men when the US military arrested him.
He was returning from a meeting to discuss swapping Afghan prisoners for money, said Pakistani Taliban commanders and intelligence officials.
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 became a trusted deputy. The two are not related. Mehsud is a common name in the region.
A US defence official said Mehsud was being lawfully held by US military forces in Afghanistan. A senior US official said the arrest did not please Afghan president Hamid Karzai, who apparently saw it as a violation of Afghan sovereignty.
A spokesman for Mr 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, whom he did not name, was then taken to an American detention facility in Bagram.