President Barack Obama tightened rules for the U.S. drone program in 2013, but he secretly approved a waiver giving the Central Intelligence Agency more flexibility in Pakistan than anywhere else to strike suspected militants, according to current and former U.S. officials.

The rules were designed to reduce the risk of civilian casualties. Mr. Obama also required that proposed targets pose an imminent threat to the U.S.—but the waiver exempted the CIA from this standard in Pakistan.

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