Ties between the intelligence agencies of Pakistan and the United States have been severely strained since the killing of Osama bin Laden in a covert U.S. raid in Pakistan in May.
Both sides have attempted to play down the tensions through public statements, but the expulsion of American security personnel by Pakistan and the suspension of some U.S. military assistance have highlighted the distrust on both sides.
In an interview with VOA, U.S. Ambassador to Pakistan Cameron Munter acknowledges that the bin Laden raid was a setback for bilateral ties.
"I think in the wake of what happened on May 2, there was a great deal of consternation on the side of Pakistan because of the issue of the sovereignty, the questions that were raised," Munter said. "There were questions that were raised in the United States because people did not know whether there was a role of Pakistani authorities in him being here. This was a source of great amount of unhappiness on both sides because there were questions that could not be answered."
But after months of their tense relationship playing out in public, this week the Pakistani military made a rare public acknowledgement that U.S. agents provided key information that helped them plan the successful raid that captured senior al-Qaida planner, Younis al-Mauritani, along with two aides.
Army spokesman Major General Athar Abbas said the authorities watched the group for months.
"We have been on alert we have been following the case since last October when it was surfaced that there is a group which will pose threat to the outside world, " said Abbas. "We have been connecting dots and therefore when we found out that they are there in the suburbs of Quetta then we conducted this raid."
The announcement is a sign the relationship is getting back on track, said Hassan Askari Rizvi, a former head of the political science department at Punjab University.
"This shows that the two agencies are now cooperating, and they need to do that because that is how they can produce results," he said. "Hopefully there will be continued cooperation and they will be able to overcome the differences that had developed between the two authorities."
The Pakistani military says al-Qaida leader al-Mauritani was mainly responsible for the network's international operations and was suspected of planning attacks on important American economic interests, including oil pipelines.
Officials have identified the other two detainees as senior operatives Abdul Ghaffar al-Shami and Messara al-Shami.
Although the arrests may help ongoing negotiations between the two sides on how to conduct future joint-operations, professor Askari Rizvi points out that important disagreements remain.
"They still diverge on certain matters whether to take action in North Waziristan and also on the issue of presence of American intelligence and security personnel in Pakistan."
Pakistan has resisted U.S. pressure to mobilize its forces against militants of the Haqqani network based in North Waziristan border region. The militants are believed to be launching cross-border raids on U.S. and allied forces in Afghanistan.
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Pakistani military authorities also have objected to the presence of U.S. Central Intelligence Agency operatives gathering intelligence about militant groups inside Pakistan.
In Washington, U.S. officials have long maintained that elements within the Pakistani spy agency have links to Taliban and al-Qaida associates. The allegation is rejected by Pakistani authorities.
But over the past decade the Pakistani agency has dispelled those suspicions by arresting dozens of senior al-Qaida operatives, said former Pakistani intelligence brigadier Asad Munir.
"All those people have been caught by the ISI with the support of CIA, so they have been working together. They have to have good relations. If there is mistrust it is directly going to affect the war on terror and if they cannot work together the [Afghan] exit strategy of [President] Obama I don't think that it will be materialized," he said.
President Barack Obama plans to withdraw all American combat forces from Afghanistan by the end of 2014. U.S. officials admit they need Pakistan's support to ensure there is a smooth transition of security responsibilities to Afghan forces.
U.S. Ambassador Munter expects the two countries will be able to re-establish their anti-terror cooperation to where it was before the bin Laden operation.
"Even though there may be a broad question, conceptually, where are we going, and what is the relationship, the body of the relationship is there and will remain there and I am optimistic that we are going to make a lot of progress in the years to come," Munter said.
U.S. intelligence officials have said in recent weeks that the death of al Qaida's chief Osama bin Laden, followed by the killing or capture of other top lieutenants have dealt a serious blow to the terrorist network.
But they have given no indication of scaling back U.S. drone strikes, which remain highly controversial in Pakistan and a continuing source of tension between the two governments.