The United States is talking with Pakistan about drone strikes as part of the countries' counter-terrorism cooperation, Kerry said during a media availability in Islamabad with Pakistani Foreign Affairs Adviser Sartaj Aziz.
During an interview with Pakistan TV, Kerry said Obama has a timeline for ending the strikes by unmanned aircraft and "we hope it's going to be very, very soon."
The comments were made available via the media pool reporter covering the trip, NBC News reported.
Kerry said Obama was very concerned about the reaction to counter-terrorism activity. "We want to work with Pakistan, not against it."
"I think the program will end as we have eliminated most of the threat and continue to eliminate it," Kerry said.
During the media availability, Kerry said Obama "has made a policy as limited and as clear as is humanly possible, and he has laid out a very transparent, accountable, thorough legal justification for any counter-terror policies the United States may or may not engage in."
The issue of U.S. counter-terrorism is sensitive because of the drone strikes on alleged Taliban and al-Qaida targets along the Afghanistan-Pakistan border region have angered Pakistanis who say it ignores the country's sovereignty.
"I know there are issues of sovereignty that are raised often," Kerry said. "I would simply remind all of our friends that somebody like an al-Qaida leader ... is violating the sovereignty of this country. And when they attack people in mosques and blow up people in villages and in marketplaces, they are violating the sovereignty of the country."
Kerry's arrival Wednesday night marked his first visit to Pakistan as secretary of state although he visited the country numerous times as a U.S. senator.
Discussing Kerry's trip, White House press secretary Jay Carney told reporters the relationship with Pakistan is "extremely important" to U.S. national security interests.
"It is a complicated but important relationship, as we've discussed in the past here," Carney said. "And I'm sure that Secretary Kerry will be having discussions with the Pakistanis about developments in their country, our joint efforts to fight terrorism -- and, as you know, Pakistanis have been among the most significant victims of terrorist attacks -- and also our efforts in Afghanistan. So I'm sure those will be among the topics of conversation that the secretary will engage in."