The US secretary of state, John Kerry, and his Pakistani counterpart, Sartaj Aziz, said on Thursday the two countries will resume high-level negotiations over security issues. Kerry suggested that disputed drone strikes could end soon.

Kerry also said he had invited Pakistan's newly elected prime minister, Nawaz Sharif, to come to Washington to meet Barack Obama.

"I'm pleased to announce that today, very quickly, we were able to agree to a resumption of the strategic dialogue in order to foster a deeper, broader and more comprehensive partnership between our countries," Kerry said, at a news conference with Aziz in Islamabad. He also said the talks would cover "all of the key issues between us, from border management to counterterrorism to promoting US private investment and to Pakistan's own journey to economic revitalization."

Kerry told Pakistani TV that the US would end strikes on Pakistan in the near future. "I believe that we're on a good track," he said. "I think the program will end as we have eliminated most of the threat and continue to eliminate it.

"I think the president has a very real timeline, and we hope it's going to be very, very soon."

The comments reflected similar statements Obama made in his foreign policy speech at the National Defense University earlier this year.

A State Department spokeswoman, Jen Psaki, said: "As we continue the transition in Afghanistan, we will no longer have the same need for force protection in the Afghan war theater and the progress we've made against core al-Qaida will reduce the need for unmanned strikes." Psaki also noted that there was "no exact timeline to provide".

The US and Pakistan launched high-level talks on a swath of security and development programs in 2010. But the talks stalled in November 2011 after US airstrikes on a Pakistani post on the Afghan border accidentally killed 24 Pakistani soldiers. Before that, the bilateral relationship was severely damaged by a variety of incidents, including a CIA contractor shooting to death two Pakistanis in the eastern city of Lahore and the covert US raid that killed Osama bin Laden in the Pakistani town of Abbottabad.

The resumption of the strategic dialogue indicates that the relationship between the two countries has improved. But there is still significant tension and mistrust, especially regarding US drone strikes and Pakistan's alleged ties with Taliban militants using its territory to launch attacks against American troops in Afghanistan.

"It is also no secret that along this journey in the last few years we've experienced a few differences," Kerry said. "I think we came here today, both the prime minister and myself, with a commitment that we cannot allow events that might divide us in a small way to distract from the common values and the common interests that unite us in big ways."

Kerry was also asked about progress on a bilateral security agreement with Afghanistan that would keep some US forces in that country after 2014.

"I am personally confident that we will have an agreement, and the agreement will be timely," he replied. "And I am confident that the president has ample space here within which to make any decisions he wants to make regarding future troop levels."

Sharif came to power in an election that marked the first time in Pakistan that a civilian government completed its full five-year term and transferred power democratically. The country has a history of civilian leaders being overthrown in military coups.

"This is a historic transition that just took place," Kerry told US Embassy employees. "Nobody should diminish it."

Senior administration officials traveling with Kerry told reporters that while relations with Pakistan have grown touchy in recent years, there is the prospect of resetting those ties with Sharif's government and working together on major issues – including counterterrorism, energy, regional stability, economic reforms, trade and investment. The officials spoke on condition of anonymity because they weren't authorized to publicly discuss Kerry's agenda.

The US wants to help strengthen the role of the civilian government in Pakistan, and wants Sharif to tackle rising extremist attacks inside his country. A prison break this week that freed hundreds of inmates raised serious questions about Pakistan's ability to battle an insurgency that has raged for years and killed tens of thousands. Suspected Islamic militants killed at least 160 people during the new government's first month in office. Sharif's government has not articulated an alternate strategy.

The US also wants Pakistan to pressure leaders of the Afghan Taliban to negotiate with Afghan president Hamid Karzai's government, renounce violence and sever ties with al-Qaida.

Officials in Afghanistan are demanding that Pakistan dismantle extremists' havens inside Pakistan and push the Taliban to join the peace process. Both the US and Afghanistan say that if attacks are allowed to continue, the region will never become stable. Pakistani officials say they do not control the Taliban, but Karzai's government is not convinced.

A protest in Islamabad against drone attacks in Pakistan's tribal belt. Photo: Muhammed Muheisen/AP

Drone strikes are another point of contention. Washington says it needs to attack dangerous militants with drones because Pakistan's government refuses to engage them militarily. Pakistan contends that the drone strikes are a fresh violation of its sovereignty, and they have increased widespread anti-American sentiment in the country.

The US has reduced the number of drone attacks against militants in Pakistan and limited strikes to top targets. These moves appear to have appeased Pakistan's generals for now, US officials said. But some officials worry about pushback from the new civilian officials, including Sharif, who wants the attacks ended. There have been 16 drone strikes in Pakistan this year, compared with a peak of 122 in 2010, 73 in 2011 and 48 in 2012, according to the New America Foundation, a US-based think tank.

After Kerry wraps up his meetings in Islamabad, he is scheduled to fly to London. The State Department said he will meet there with the United Arab Emirates foreign minister, Abdullah bin Zayed Al-Nahyan, to discuss Egypt, Syria and Middle East peace.