Saleem Shahzad

A prominent Pakistani journalist who investigated links between the military and al-Qaida has been found dead, triggering angry accusations against the powerful Inter-Services Intelligence spy agency.

Saleem Shahzad, Pakistan correspondent for a news service based in Hong Kong, disappeared on his way to a television interview in Islamabad on Sunday evening. On Tuesday ,police said they found his body on a canal bank in Mandi Bahauddin, 80 miles south-east of the capital.

Shahzad's abandoned car was found 25 miles away. Television images of his body showed heavy bruising to his face. Media reports said he had a serious trauma wound to the stomach.

Human Rights Watch had already raised the alarm over the disappearance of the 40-year-old father of three, citing a "reliable interlocutor" who said he had been abducted by ISI.

"This killing bears all the hallmarks of previous killings perpetrated by Pakistani intelligence agencies," said a senior researcher for Human Rights Watch in south Asia, Ali Dayan Hasan. He called for a "transparent investigation and court proceedings".

Other journalists reacted angrily, directly accusing ISI of responsibility on television and social media. "Any journalist here who doesn't believe that it's our intelligence agencies?" tweeted Mohammed Hanif, a bestselling author.

"We want an answer. We need an answer. We deserve an answer," said talk-show host Quatrina Husain.

A senior ISI official told the Associated Press that allegations of the agency's involvement were absurd.

Shahzad, who worked for the online service Asia Times Online and the Italian news agency Adnkronos, vanished two days after publishing a story alleging Pakistan military officials had been in secret negotiations with al-Qaida.

The story claimed the terrorist group had attacked the Mehran naval base in Karachi on 22 May after talks with the military to release two naval officials accused of militant links broke down.

The naval base assault was a humiliation for the Pakistani army, which battled for 17 hours against at least four heavily armed men who blew up two US-built surveillance planes and killed 10 soldiers. On Tuesday, Pakistani media reported that military intelligence had picked up a retired navy commando and his brother in Lahore in connection with the raid.

The raid came after unprecedented criticism of the army for the US raid that killed Osama bin Laden, and WikiLeaks disclosures that showed army complicity with the CIA drone programme.

Shahzad was abducted from central Islamabad on Sunday as he travelled to the studios of Dunya television to discuss his report on the naval base attack. His wife alerted human rights groups.

He had previously warned of threats to his life from ISI, according to Human Rights Watch. Last October, after he was summoned to ISI headquarters to explain a story, he sent an email to be released in the event of his death, Hasan said.

The email recounted a meeting with two senior ISI personnel who questioned him over a story about Mullah Brader, a Taliban commander captured in Pakistan with American help months earlier.

The two ISI officials named in the article, Rear Admiral Adnan Nazir and Commodore Khalid Pervaiz, were naval officers. Shahzad claimed that Nazir warned the journalist that he might find himself on a "terrorist hitlist". "If I find your name in the list, I will certainly let you know," he reportedly said.

Last week, Pervaiz was made commander of the Karachi naval base that was attacked.

"We believed [Shahzad's] claim that he was being threatened by the ISI was credible and any investigation into his murder has to factor this in," said Hasan.

As a reporter, Shahzad was known for delving deep into the murky underworld of Islamist militancy. He had interviewed some of the most notorious leaders, including Sirajuddin Haqqani, a major player in the Taliban insurgency in Afghanistan, and Ilyas Kashmiri, a Pakistani militant who works for al-Qaida.

He had just published a book called Inside Al-Qaeda and the Taliban: Beyond Bin Laden and 9/11.

Zaffar Abbas, editor of Dawn, Pakistan's most respected paper, paid tribute to Shahzad as "a fine reporter, one of a breed of Pakistani journalists who really believe in investigative journalism". In the light of the death, he is was looking at scaling back his own paper's coverage.

"I am seriously considering the entire process of reporting, and to what extent I can put my own team at risk. It is becoming increasingly dangerous for people to openly report, whether militants or security agencies are involved."

Pakistan's prime minister, Yousaf Raza Gilani, expressed his "deep grief and sorrow" over Shahzad's death and ordered an inquiry, saying that "the culprits would be brought to book at every cost".

Hopes for any inquiry, however, were low. Although the ISI technically reports to Gilani, in reality it is controlled by the army chief, General Ashfaq Kayani. Although accused of numerous human rights abuses over the years, serving ISI officials have never been prosecuted.

Cricketer turned politician Imran Khan termed Shahzad's death a "heinous crime" but avoided mention of the ISI, instead blaming the "servile policies [of] a corrupt and inept government".
Pakistan is the world's most dangerous country for journalists, according to Reporters without Borders, which says that 16 journalists have been killed in the past 14 months. Some of the worst excesses occurred in western province of Balochistan.

Last September Umar Cheema, another investigative reporter, was abducted from Islamabad for six hours and tortured before being released. He said he suspected that his kidnappers belonged to the ISI.

Shahzad was buried in an unmarked grave on Monday, after local police failed to identify his body. His remains were exhumed on Tuesday on orders from President Asif Ali Zardari's office. An autopsy is due.