“You cannot say that we are important allies and then you are negotiating with people whom we are hunting and you don’t include us,” he said.

An American official in Washington who has been briefed on the arrest denied that there had been negotiations with the Taliban commander or that Pakistani intelligence engineered the arrest to ensure a role in negotiations. “That’s a conspiracy theory to which I give no credit, because it’s just not true,” the official said.

But whether or not that was Pakistan’s intention, it may be the effect.

The Taliban are longtime Pakistani allies in Afghanistan, and Pakistan has signaled its interest in preserving influence there.

Though the Obama administration has been divided on whether and how to deal with the Taliban, the Pakistani move could come at the expense of the Afghan government of Hamid Karzai and complicate reconciliation efforts his government has begun.

Image Marines in Marja, Afghanistan, where the military is investigating civilian deaths. Credit... David Guttenfelder/Associated Press

An American intelligence official in Europe conceded as much, while also acknowledging Mullah Baradar’s key role in the reconciliation process. “I know that our people had been in touch with people around him and were negotiating with him,” the official said, speaking on the condition of anonymity because he was not authorized to discuss the issue.

“So it doesn’t make sense why we bite the hand that is feeding us,” the official added. “And now the Taliban will have no reason to negotiate with us; they will not believe anything we will offer or say.”