A Pakistani journalist who had written about alleged links between the nation’s navy and the al-Qaeda terrorist network was found dead in an abandoned car near the capital city of Islamabad.

Saleem Shahzad, 40, worked for the Italian news agency Adnkronos and for Hong Kong-based Asia Times Online (ATO). He went missing on Sunday after he left his home to participate in a television interview.

According to Pakistani officials, Shahzad’s body was discovered near his car in the town of Sarai Alamgir, 93 miles southeast of Islamabad. His body was identified by relatives. There were indications he had been tortured.

Two days prior to his disappearance, Shazad wrote an article for ATO in which he alleged that an attack on a Pakistani naval base in Karachi last week was perpetrated by al-Qaeda in retaliation for the prior arrest of naval officials on charges they were connected to the terrorist group.

The story that Shahzad wrote also suggested strongly that al-Qaeda attacked the naval base because its negotiations with the Pakistan navy had ruptured.

During that attack, which lasted almost a whole day, six militants destroyed two US-made surveillance aircraft and killed ten security personnel. At the time, Pakistan’s Taliban claimed responsibility for the act, saying it was revenge for the US killing of Osama bin Laden in Pakistan.

According to Dawn, an English language Pakistani daily, Ali Dayan Hasan, senior South Asia researcher at Human Rights Watch (HRW), said Shahzad had earlier complained that Pakistan’s Inter-Services Intelligence (ISI) agency has threatened him.

“The other day he visited our office and informed us that ISI had threatened him. He told us that if anything happened to him, we should inform the media about the situation and threats,” Hasan told Agence France Presse.

“We can form an opinion after the investigation and a court verdict, but… in the past the ISI has been involved in similar incidents.”

HRW believed he was indeed arrested and possibly murdered by Pakistani intelligence agents.

While Shahzad was missing, The Human Rights Commission of Pakistan feared for his safety and cited “exceedingly disturbing” reports that he might have been kidnapped by a state agency.

Meanwhile, Pakistan’s Prime Minister Yousuf Raza Gilani ordered an investigation into Shahzad’s kidnapping and murder, vowing that the guilty parties would be “brought to book”.

Shahzad was no stranger to danger.

In 2006, he was kidnapped by Taliban agents in Helmand, southern Afghanistan who accused him of being a spy. They released him free after seven days.

Reporters Without Borders has stated that Pakistan is one of the most dangerous places on earth in which to be a journalist, citing that 11 reporters were killed in the country last year.