The U.S. official's figures echo similar ones cited in June by White House counterterrorism adviser John Brennan.
American drone strikes in Pakistan have inflamed tensions between the two countries, especially after attacks in which civilians were killed.
A drone strike March 17 reportedly hit a community council meeting in North Waziristan, one of the seven districts of Pakistan's volatile tribal region bordering Afghanistan. It killed 44 people - mostly civilians, two Pakistani sources have said. That strike prompted protests in Pakistan, and the United States temporarily suspended its drone attacks.
U.S. officials rarely discuss publicly the CIA's drone program in Pakistan, though privately, officials have said the covert strikes are legal and an effective tactic in the fights against extremists.
But the allegations by the Bureau of Investigative Journalism spurred reaction from U.S. officials, who are mindful of often violent reaction in the region to allegations of civilian casualties.
The State Department also disputed the group's findings, saying the United States goes to "enormous lengths to avoid killing or injuring innocent civilians."
"To that end, President (Barack) Obama has directed that we be exceptionally precise and surgical in addressing the terrorist threat, relying both on rigorous review procedures and all of the technological tools at our disposal to ensure that innocent civilians are protected," said Victoria Nuland, a State Department spokeswoman.
"We try to ensure that we only use force against those individuals who threaten us."
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