|Mullen, left, and Pakistan's General Khalid Shameem Wynne discussed ISI's ties with Afghan fighters [AFP/HO/ISPR]
The US will maintain its drone programme in Pakistan but the way forward will be determined by both sides, an unnamed US military official has said.
The issue has been a bone of contention between the two nations, with some Pakistani officials calling for sharp cuts in drone attacks.
"The [programme] is something that we have said we go ahead on. The question is how," the official said on condition of anonymity.
"And that process is going to be something that's going to be one of the main tasks that our intel and our military guys have."
The matter was raised last week in Washington in talks between Leon Panetta, the CIA director, and Lieutenant-General Ahmed Shuja Pasha, the chief of Pakistan's Inter-Services Intelligence (ISI) agency.
"I'll pause from my normal optimism and say this is a tough one. This is a real tough one," the unidentified US official said.
"Because that has been so inflamed in the public that the ability of our intelligence and our military guys to get together and say 'what's our common ground here?' is limited."
The long-running issue of the US drone strikes on targets in Pakistan's tribal areas has kept tensions high between the two countries regarding the US' role in the region.
The covert drone-launched missile strikes that target fighters in Pakistan's lawless border areas have stoked anti-American sentiment among the populace, even though it is widely believed that the strikes occur with the tacit consent of Islamabad.
Publicly, Pakistan's leaders have insisted that the drone strikes stop and that the US share the Unmanned Aerial Vehicle (UAV) technology with Pakistan so that it can take operational control of them, but US officials say operations will continue in order to achieve US security objectives.
US officials have privately said in the past that Washington would not consider demands by some Pakistani officials for sharp cuts in drone attacks.
Al Jazeera's Kamal Hyder, reporting from Islamabad, said the remarks about continued US drone attacks came as a surprise especially when the strikes are widely unpopular in Pakistan.
"Right now the issue is being taken up even at the International Court of Justice because the government officials and some major leaders of religious parties are saying that the Americans have no mandate to cross into Pakistani sovereign territory," he said.
"There is a lot of top talking to do and a lot of protests expected over the continued US policy on drone strikes."
The remarks on the drone programme also came as a high-level US military officer accused Pakistan's intelligence service of maintaining ties to armed fighters in Afghanistan.
"Haqqani is having a much more difficult time now. We're still working through the [Pakistani] military support, the way through the relationships the [ISI] has with the Haqqani network, and the strain that creates"
Admiral Mike Mullen, chairman, US Joint Chiefs of Staff
Admiral Mike Mullen, the chairman of the US Joint Chiefs of Staff, made the comments on Wednesday during a trip to Islamabad. He was in Afghanistan a day earlier.
In a statement, Mullen praised co-operation between US and Pakistani troops working in joint operations against fighters belonging to the Haqqani network, who target NATO forces in eastern Afghanistan.
He did acknowledge, however, that there were also a "strain" due to Taliban and other fighters' alleged ties with Pakistan's ISI.
"Haqqani is having a much more difficult time now," Mullen said, according to an article on the joint chiefs of staff website.
"All that said, we're still working through the [Pakistani] military support, the way through the relationships the [Pakistani intelligence agency] has with the Haqqani network, and the strain that creates.
"I'll see General Kayani here shortly and these are issues I address with him every single time we engage. And I certainly intend to [raise that] this week."
The JSC chief's trip to Pakistan is the latest in a series of high-level meetings that have followed the fatal shooting in January of two Pakistanis by Raymond Davis, a CIA security contractor, who said he was acting in self-defence.
'A lot of mistrust'
Pakistan is a crucial ally of the US in the war in Afghanistan, and receives billions of dollars in military and civilian aid from the country.
Zafar Jaspal, an Islamabad-based security analyst, told Al Jazeera that it was unlikely that Mullen's trip would do much to ease the tension, as most of Pakistan's objections are related to CIA activities in the country, and he does not have command of that agency.
"There is a lot of mistrust in this relationship, which the United States and Pakistan want to overcome, but at the same time ... though both sides have been working a lot, but still the rapprochement approach is not giving us an optimistic picture or outlook," he said.
"Their interdependency is too [high], especially in the context of political and security instability in Afghanistan, and at the same time Pakistan is getting some assistance from the United States. But if you recall [on Monday] Pakistan's finance minister [Abdul Hafeez Shaikh] said that we are not getting as much as is expected, or generally people think."
Jaspal said that the US has been pushing Pakistan to take on Haqqani group fighters and suspected al-Qaeda sanctuaries in North Waziristan, but the Pakistani government has responded in the negative, citing a lack of resources.