Kerry told reporters in Kabul the suspect, who was captured by U.S. forces Oct. 5, was wanted in the United States in connection with a plot to bomb Times Square in 2010 and was a fairly routine operation.
"We will absolutely work with the government of Afghanistan to cooperate so that the appropriate process flows out of this, to respect their interests and respect their sovereignty," said Kerry. "But this was a normal counter-terrorism procedure, according to the standards that we have been operating by for a long period of time."
The capture of Latif Mehsud was seen as a fly in the ointment of the negotiations to craft a new security agreement that will govern U.S.-Afghan relations as American troops wind down their long-running mission.
The Washington Post said respect for Afghan laws and jurisdiction over remaining U.S. forces has been a ticklish subject. Afghan intelligence and security officials protested the capture, saying Mehsud was in their custody when he was forcibly taken by American forces.
Kerry said he and Afghan President Harmid Karzi had ironed out the issue Sunday. "We followed the normal procedures that the United States follows in our agreement," he said. "We regret that this circumstance took place in some ways that some folks apparently the chain of communication didn't go as far. But we did what we are supposed to do under the agreement."
Karzai said the new agreement, which will be presented to a conference of Afghan tribal leaders next week, guarantees respect for Afghan sovereignty and that Washington would have to take it seriously.
"Our discussion today in particular has been focused on making sure that through the Bilateral Security Agreement, we make sure that such violations are not repeated," Karzai said. "If they [the United States] want to be partner with us, this partnership must completely guarantee sovereignty and security of Afghanistan. We receive this through our document, but the rest will be up to the Afghan government and our friends, and in order to build on this, based on mutual respect and friendship."
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