Pakistani journalists and politicians pray to pay tribute to late journalist Saleem Shahzad in Islamabad on June1, 2011. Hundreds of mourners turned out for the burial of a Pakistan journalist who had said he was being threatened by the country's intelligence services before he was tortured to death. – AFP Photo 

ISLAMABAD: A prominent Pakistan journalist may have been tortured to death for exposing growing links between the country's intelligence agencies and militants who appear to be infiltrating every state institution, a leading human rights activist said on Thursday.

Saleem Shahzad, who worked for Hong Kong-based Asia Times Online, disappeared from Islamabad on Sunday. His body was found in a canal two days later with what police said were torture marks.

Zohra Yusuf, head of the independent Human Rights Commission of Pakistan (HRCP), added to intense speculation that the military's Inter-Services Intelligence (ISI), one of the most powerful institutions in a country with a weak civilian government, may have had a hand in the death of Shahzad, a father of three.

“We don't have any conclusive evidence. But the circumstances seem to point to state security agencies because there have been other cases where journalists have been picked up. It's a very disturbing trend,” she told Reuters.

“Perhaps he was being tortured to reveal his sources and his contacts. He could have died in the process.”

Pakistan is the world's most dangerous country for journalists, according to Reporters Without Borders, and Shahzad was one of the most high profile Pakistani journalists to be killed so far.

Pakistani authorities deny any collusion with militants. The ISI rejected suggestions of its involvement in Shahzad's murder and criticised the media for jumping to that conclusion.

Analysts have not ruled out the possibility that militants kidnapped and killed Shahzad. He wrote extensively about al Qaeda and other groups.

Human Rights Watch, however, said Shahzad, 40, had voiced concern about his safety after receiving threatening telephone calls from the ISI and was under surveillance since 2010.

Before he was killed, Shahzad had been investigating the alleged ties between militant groups and Pakistan's powerful security establishment, an issue that was put in the spotlight after the killing of Osama bin Laden in Pakistan in May.

The military and ISI were deeply embarrassed by the discovery of the al Qaeda leader in a garrison town about a two-hour drive from Islamabad and angered by the fact that he was killed in a secret U.S. raid.

US officials said they did not inform the Pakistani authorities for fear that their plans be compromised, and both Washington and Islamabad said bin Laden must have had a support network that enabled him to hide in Abbottabad for many years.

A brazen militant attack on a key naval airbase in Karachi a few weeks ago also bore the hallmarks of an inside job, and security officials said an a sacked navy officer and his brother had been arrested in connection with the assault.

Before his death, Shahzad had written a story claiming the al Qaeda had attacked the PNS Mehran base after the failure of negotiations with the military to release two naval officials accused of militant links.

Yusuf said she was worried that militants appear to be gaining ground in various state institutions, which would further destabilise the nuclear-armed South Asian nation afflicted with weak governance, a stagnant economy and lack of development -- conditions that can encourage disillusioned young men to join groups like the Taliban or al Qaeda.

“It seems that now every institution has been infiltrated (by militants). It's been a slow process, it's been happening gradually,” she said. “These are very dangerous developments.”

Yusuf said human rights activists also have to tread cautiously in Pakistan, where she says extrajudicial killings are on the rise, especially in regions such as Baluchistan where security forces are fighting a low-level insurgency.

“In Baluchistan itself we lost two of our activists,” she said. “One was picked up last December by security agencies and his body was recovered in April this year. In March again this year another of our activists was shot dead.”

The Human Rights Commission of Pakistan estimates over 1,000 people, mostly political opponents of the government and Baluch nationalists, have gone missing over the last 10 years.

The commission had named dozens of missing people in a Supreme Court petition that holds intelligence agencies responsible for their fate, Yusuf said. “The Supreme Court summoned them. They have appeared a few times and said they don't know. Sometimes they don't appear at all.”