An Afghan store clerk shows a calendar with pictures of Afghan leaders including Mohammad Omar. (Barialai Khoshhal/AP)

In early 2011, then-CIA Director Leon Panetta confronted the president of Pakistan with a disturbing piece of intelligence. The spy agency had learned that ­Mohammad Omar, the Taliban leader who had become one of the world’s most wanted fugitives after the Sept. 11, 2001, attacks, was being treated at a hospital in southern Pakistan.

The American spy chief even identified the facility — the Aga Khan University Hospital in Karachi — and said the CIA had “some raw intelligence on this” that would soon be shared with its Pakistani counterpart, according to diplomatic files that summarize the exchange.

U.S. intelligence officials now think that Omar probably died two years later, in 2013, and Afghan officials said this week that he succumbed while being treated for a serious illness in a Karachi hospital, just as those earlier intelligence reports had indicated.

The belated disclosure this week of Omar’s death has added to the legend of the ghostlike Taliban chief, a figure so elusive that it appears to have taken U.S. spy agencies two years to determine that one of their top targets after 9/11 was no longer alive.

Afghan officials say that Taliban leader Mohammad Omar died in a hospital in Karachi, Pakistan, more than two years ago. (The Washington Post)

But the emerging details of Omar’s death may also help explain the extent to which his ability to remain both influential and invisible was a reflection of the competing and often hidden agendas in the counterterrorism partnership between the United States and Pakistan.

Current and former U.S. ­officials said that despite intermittent intelligence on Omar’s whereabouts, there was never a concerted push to find him that remotely approached the scale of the manhunt for al-Qaeda leader Osama bin Laden.

At the same time, the one-eyed Taliban leader’s apparent ability to get medical treatment in the port city of Karachi has bolstered long-standing suspicions that Omar was being sheltered by Pakistan.

Milt Bearden, a former CIA operative in Pakistan and Afghanistan, said that “it is beyond puzzling” that Omar’s death could go unconfirmed for so long, especially given the intelligence and surveillance capabilities of the United States.

But “it’s another case of why intelligence collection in that part of the world is so difficult,” Bearden said. “The truth is layered, and there are multiple agendas, none of which we ever really understand.”

U.S. intelligence agencies have not yet corroborated claims by Afghan authorities that Omar died in a Karachi hospital, but they noted that Pakistan’s ­Inter-Services Intelligence agency had ties to the Taliban dating back to the 1980s, when the ISI served as a conduit for U.S. arms and money to Islamist militants fighting the Soviets in Afghanistan.

A Pakistani official described claims that Omar died in Pakistan or that the government was even aware of his presence in the country as “unfounded speculation.”

Hafiz Saeed, leader of Pakistan’s religious group Jamaatud Dawa, front, leads a funeral prayer for Taliban leader Mohammad Omar at a mosque in Lahore, Pakistan. (Ahmed Ali/AP)

“There is no certainty about the date or place of his death,” said Nadeem Hotiana, a spokesman for the Pakistan Embassy in Washington. Hotiana noted that a statement released by the Taliban on Thursday confirming Omar’s death “categorically mentions that Mullah Omar never left Afghanistan.”

U.S. officials attributed the belated determination that Omar had died to a range of factors, including the extremely reclusive nature of a figure for whom there is only one widely circulated photograph. The officials also noted the frequency with which rumors of his demise had been previously proved wrong.

Omar was said to be afflicted with illnesses ranging from kidney failure to meningitis. U.S. officials said intelligence analysts began to suspect Omar had died a year or more ago but reached that conclusion only more recently, based on new information as well as a gradual accumulation of evidence.

The CIA declined to comment on Omar’s death or the exchange between Panetta and then-
Pakistani President Asif Ali Zardari described in diplomatic documents obtained by The Washington Post.

Their meeting in January 2011 came when Zardari was in the United States to attend a memorial service for U.S. diplomat Richard Holbrooke.

Former U.S. and Pakistani officials said Panetta’s disclosure was designed in part to prod Pakistan to detain Omar but also to serve notice that the CIA was aware of the Taliban leader’s presumably sanctioned presence in Pakistan.

Other U.S. officials also made clear in other meetings their belief that Pakistan was protecting Omar and other elements of the Taliban. In Islamabad in 2011, Vice President Biden warned then-Prime Minister Yousuf Raza Gilani that relations with Afghanistan wouldn’t improve until Pakistan answered difficult questions including “what do we say about Mullah Omar,” according to a separate diplomatic document.

In 2010, during a briefing with Pakistani officials on a White House strategy review for the region, Lt. Gen. Douglas Lute said that “while Pakistan has done a lot to deny safe havens to terrorists . . . senior leadership of the Quetta Shura including Mullah Omar resides between Karachi and Quetta,” according to a third diplomatic document.

Current and former U.S. officials said they knew of no effort by the CIA to mount an operation to apprehend Omar even after learning he may have been in declining health in a Karachi hospital.

The agency also had other pressing priorities at the time. Among them was seeking to confirm the location of bin Laden at a compound in Abbottabad, Pakistan, that was the site of a raid by U.S. Navy SEALs four months later.

The pace of the CIA’s drone campaign in Pakistan was a growing source of friction with Pakistan. And just two weeks after the Panetta-Zardari meeting, CIA contractor Raymond Davis was taken into custody after killing two Pakistani men in a shootout on a bustling street in Lahore.

Even before those events, officials said, the CIA’s hunt for Taliban figures never matched the intensity of its pursuit of ­al-Qaeda.

“We were overwhelmingly focused on al-Qaeda, and there were many fewer instances where we had what we thought was halfway-reliable information on the whereabouts of senior members of the Taliban,” said Robert Grenier, the former CIA station chief in Pakistan and former head of its Counterterrorism Center.

There was also a clear limit to the cooperation from the ISI.

“Pretty quickly you could see a pattern,” Grenier said. “Where the ISI was very effective working with us in tracking down ­al-Qaeda, anytime we had a lead on a senior member of the Taliban, the Pakistanis weren’t successful in following up.”

Pakistan also repeatedly rebuffed requests by the CIA to send drones over Quetta, the city where Taliban leaders were based after fleeing Afghanistan in 2001. When a senior Taliban figure was detained in 2010, it was only by accident. U.S. officials said Pakistan didn’t know Abdul Ghani Baradar was present at a Karachi compound when he was arrested, and he was released in 2013.

A former Pakistani official said parts of the government may have sought to keep Omar’s death secret out of fear that Taliban factions would splinter without him and damage Islamabad’s ability to influence peace talks with Afghanistan.

The former official said there was even internal deception. The former official said the ISI told Pakistani leaders in March this year “that Mullah Omar is seriously ill and his condition is deteriorating.”

Missy Ryan contributed to this report.