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Officials say Mehsud was arrested as he was driving along a main highway in the eastern province of Khost.
A senior Pakistan Taliban commander dubbed a "terrorist leader" by the US government has been captured in Afghanistan.
Latif Mehsud was captured on October 5 and taken to the Bagram military base near Kabul.
His capture is a major blow to Tehrik-e-Taliban Pakistan (TTP), or Pakistani Taliban.
Arsallah Jamal, the governor of eastern Logar province, told the Associated Press on Friday that Mehsud was arrested by American forces as he was driving along a main highway in the Mohammad Agha district
TTP confirmed the capture but said instead that Mehsud was captured by the Afghan army at the Ghulam Khan border crossing in the eastern province of Khost.
The Pakistani Taliban also said Mehsud was returning from talks to discuss a failed prisoner swap deal.
The US State Department confirmed the senior commander was captured but did not clear up any of the details.
"Latif Mehsud is as a trusted confident of the group's leader, Hakimullah Mehsud," spokesperson Marie Harf said of the men who are not related.
"TTP claimed responsibility 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 capture is said to have angered Afghan President Hamid Karzai, who saw the move as a violation of Afghan sovereignty.
Karzai met with US Secretary of State John Kerry, who made a surprise trip to Afghanistan this week.
The two men continued talks on Saturday over a deal that would keep US troops in Afghanistan after 2014.
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