WASHINGTON — Less than a week after President Obama outlined a new direction for the secret drone wars, Pakistani officials said that a C.I.A. missile strike on Wednesday killed a top member of the Pakistani Taliban, an attack that illustrated the continued murkiness of the rules that govern the United States’ targeted killing operations.

The drone strike in Pakistan’s tribal belt, along the Afghan border, was the first since Mr. Obama announced what his administration billed as sweeping changes to the drone program, with new limits on who would be targeted and more transparency in reporting such strikes.

But in the days since the president’s speech, American officials have asserted behind the scenes that the new standards would not apply to the C.I.A. drone program in Pakistan as long as American troops remained next door in Afghanistan — a reference to Mr. Obama’s exception for an “Afghan war theater.” For months to come, any drone strikes in Pakistan — the country that has been hit by the vast majority of them, with more than 350 such attacks by some estimates — will be exempt from the new rules.

American officials refused to publicly confirm the drone strike or the death of the Pakistani Taliban’s deputy leader, Wali ur-Rehman, even as Pakistani government and militant figures reported that he had been killed. Thus, the promise of new transparency, too, seemed to be put off.