Syed Saleem Shahzad, who investigated al-Qaeda's alleged infiltration of the navy and told a rights activist he'd been threatened by the country's intelligence agencies, was found dead in Islamabad. (Cristiano Camera/The Associated Press, Courtesy of Adnkronos)

Last week, a prominent Pakistani investigative reporter published an article alleging that al-Qaeda had infiltrated Pakistan’s navy and carried out the recent attack on a naval air base. On Tuesday, the journalist’s body — his face severely beaten — was found 100 miles from his home in this capital city, two days after he disappeared.

Syed Saleem Shahzad’s killing, other journalists and human rights activists said they suspected, was payback — not from militants, but from Pakistan’s fearsome spy agencies. Shahzad had written before about their dealings with Islamist insurgents, and he had said that intelligence officers had warned him.

“I am forwarding this email to you for your record only if in case something happens to me or my family in future,” Shahzad, 40, wrote in October to the Pakistan representative of Human Rights Watch, sharing details of a meeting he had just had with officers from the Inter-Services Intelligence agency, or ISI. Shahzad suggested that they had threatened him, an experience that Pakistani journalists, activists and politicians say is not uncommon.

But those threats rarely end in killing, and Shahzad’s death immediately sparked fresh criticism of Pakistan’s intelligence apparatus. The “agencies,” as they are known here, last month faced unusual public condemnation for their apparent failure to locate Osama bin Laden in a garrison city, as well as allegations that they had harbored him.

On Tuesday, the focus was on activities Pakistan’s spies are better known for domestically: punishing those who cross the influential military, the main locus of power in a nation with a weak civilian government.

An ISI official denied that the agency was involved in Shahzad’s death. “Show us the proof. Otherwise, it’s totally absurd,” the official said, noting that Shahzad’s coverage might also have angered militant organizations. Pakistan’s interior minister, Rehman Malik, told journalists that the motive appeared to be “personal enmity.”

Shahzad’s killing also renewed attention on the alleged crossover between militants and Pakistan’s security forces, some of which he outlined in a recent article for the Hong Kong-based Asia Times Online, for which he was the Pakistan bureau chief. According to Shahzad’s reporting, last week’s attack on a Karachi naval base was a response to the Pakistani navy’s detection of al-Qaeda cells within its ranks, and it followed failed discussions between the navy and al-Qaeda about the release of naval officers arrested on suspicion of links to the terrorist group.

On Monday, Pakistani media reported that a former navy commando had been detained for questioning in the attack.

U.S. intelligence analysts are skeptical that al-Qaeda has penetrated Pakistan’s armed forces. “There’s not likely to be an organized al-Qaeda cell within the Pakistan navy,” a U.S. official said.

But U.S. officials said that there is a long-standing concern over the presence of Islamist militants — what one official referred to as “onesies and twosies” — among Pakistan’s military branches. Pakistan’s leaders privately share this concern, U.S. officials said.

On the radar

Shahzad, the author of a new book on al-Qaeda and the Taliban, was considered well connected to both the military establishment and militant groups. He persisted though the ISI had warned him several times about articles it “deemed detrimental to Pakistan’s national interests or image,” according to Asia Times Online.

In October, Shahzad told Human Rights Watch, the ISI summoned him over an article that said Pakistan had released Abdul Ghani Baradar, an Afghan Taliban commander arrested in Karachi in early 2010, so that he could play a part in reconciliation talks in Afghanistan. An ISI official asked Shahzad to identify his source and write a denial; Shahzad said he declined, allowing only that the story was leaked by intelligence and confirmed by “the most credible” Taliban source.

Then, Shahzad said, the official added what he called a “favor,” telling him that a militant had recently been arrested.

“The terrorist had a hit list with him,” the ISI official said, according to Shahzad’s written account. “If I find your name on the list I will certainly let you know.”

Shahzad disappeared Sunday evening as he drove through a genteel sector of Islamabad on the way to an interview at a television station. Before his body was found, Human Rights Watch said “credible sources” said they thought that he had been abducted by intelligence agents but that the sources indicated Shahzad would be released. Instead, police announced Tuesday that his body had been found, and photos aired on television indicated he had been beaten.

Pakistani Prime Minister Yousaf Raza Gillani condemned the killing and ordered an investigation.

Ali Dayan Hasan, the Pakistan representative for Human Rights Watch, said it would have been difficult for anyone unaffiliated with the security agencies to abduct a man and his car from Islamabad, a city riddled with police checkpoints.

More important, he and journalists said, Shahzad’s disappearance and treatment bore the hallmarks of Pakistan’s intelligence agencies — a topic few here are willing to discuss openly. Politicians whisper about being harassed and spied on. Nationalist activists in the province of Ba­luchistan, whom the security establishment views as insurgents, are regularly abducted or killed.

In April, the main opposition party, the Pakistan Muslim League-N, sharply criticized the spy agencies and vowed to bring evidence about their extralegal activities to Parliament. In a recent interview, however, opposition leader Chaudhry Nisar Ali Khan said it would not be “appropriate” to detail those allegations until the government asked for them, which it has not.

“There should not be states within states. There should not be parallel policies being run by intelligence agencies,” he said.

Of the intelligence services, a Pakistani government official said: “They have two purposes in life: one is keeping control at home, and the other is the five letters,” a reference to the Pakistani military’s main foe, India.

Inhibiting newsgathering

In a nation where the big story is Islamist insurgency and the military’s fight against it, local journalists regularly receive threats from both sides, Hasan said. As a result, few journalists among Pakistan’s boisterous press corps are willing to openly criticize the military.

“It is becoming very dangerous indeed for journalists to perform their professional duties,” Hasan said.

Pakistan was the world’s most dangerous place for journalists in 2010, according to the Committee to Protect Journalists, which said eight reporters were killed, most of them in militant attacks. Other journalists were abducted, including Umar Cheema, an investigative reporter for the News, an English-language daily.

Cheema, who has written several articles scrutinizing the army, says he was kidnapped from Islamabad and beaten for six hours. He has since spoken out about his ordeal, which he said he has determined was carried out by the ISI. In an interview, Cheema said he harbored doubts that the agency would go so far as to kill Shahzad. Nevertheless, he said, he and his colleagues feel more vulnerable.

“It’s a very strong message to the journalist community,” Cheema said. “If the ISI is not involved, they should come up with some evidence who has done it. Just denying it won’t work. It won’t remove the suspicions of the people.”

Staff writer Greg Miller in Washington contributed to this report.