"In no way would we ever deprive ourselves of a tool to fight a threat if it arises," the State Department said, hours after Kerry said there was a "timetable" to end the strikes, The New York Times reported Friday.
In an interview Thursday in Pakistan, Kerry said he hoped the drone strikes in the country's western mountains would end "very, very soon."
His comments would appear to run counter to the Obama administration's policy on drones.
"There's nothing that indicates this administration is going to unilaterally end drone strikes in Pakistan, or Yemen for that matter," said Micah Zenko, a fellow with the Council on Foreign Relations.
Obama has pledged greater accountability and transparency for the drone program, but he and others in the administration refuse to talk publicly about specific strikes.
The use of drones appears to be on the increase. The Bureau of Investigative Journalism, which monitors drone strikes, said there were three drone strikes in Pakistan last month, the most since January.
Overall, the number of drone strikes has declined in the last four years.