Prominent journalist Syed Saleem Shahzad, who went missing in the Pakistani capital over the weekend, was found dead in Punjab province on Tuesday with his body bearing marks of torture, police said.

Two days before he went missing, Shahzad had written an article in which he contended that Al Qaida attacked a naval airbase in Karachi after failed talks with the navy to release some arrested naval personnel who had terror links.

Shahzad, 40, was the Pakistan bureau chief for Asia Times Online and a correspondent for Italian news agency Adnkronos International.

Shahzad, the author of ‘Inside Al Qaida and Taliban: Beyond Bin Laden and 9/11,’ had alleged the attack was mainly in response to an internal clampdown on Al Qaida affiliates within the Pakistan Navy.

He was reported missing on Sunday evening shortly after he left his home in Islamabad for a television station to record a programme. Reports earlier in the day said a body had been found near Shahzad's car at Sarai Alamghir near Jhelum town, about 200km from Lahore.

After police informed Shahzad's family, a relative went to the site and identified his body. Police said Shahzad's body bore marks of torture. An autopsy report stated that there were marks of torture on Shahzad's torso and face, Geo News channel reported.

The channel beamed a black and white photo of the journalist's face with visible injuries. An Islamabad Police spokesman too confirmed that Shahzad's body had been found in a canal.

A murder case had been registered and his body was buried after an autopsy, the spokesman said. Rights groups, including Human Rights Watch, had said shortly after Shahzad was reported missing that they believed he was in the custody of Pakistani intelligence agencies.

The International Federation of Journalists and the Pakistan Federal Union of Journalists had appealed to the government to order security agencies to trace Shahzad. No group claimed responsibility for the killing and Shahzad's family said he had no enmity with anyone.

Shazad had shifted from Karachi to Islamabad two years back and his reporting mostly focussed on militant organisations, including banned groups and Al Qaida. The report said naval intelligence had traced an Al Qaida-linked cell operating inside several naval bases in Karachi, Pakistan's largest city and key port.

Micro-blogging website Twitter was flooded with reactions expressing shock as soon as news broke of Shahzad's death.

Farahnaz Ispahani, a spokesperson for President Asif Ali Zardari, wrote: "A terrible sickness has permeated our society. Saleem Shahzad was a friend, colleague and intrepid reporter. Answers are needed."

Prime Minister Yousuf Raza Gilani expressed ‘deep grief and sorrow’ over the death of Shahzad and ordered an immediate inquiry into his kidnapping and murder.

Gilani said those responsible for the killing ‘would be brought to book at every cost.’ "The present government strongly believes in the freedom of expression and considers freedom of media as an essential ingredient to strengthen democratic values and culture," he said.

Months before his death, Shahzad sent an email to Ali Dayan Hasan of Human Rights Watch in October 2010 with the words: "I am forwarding this email to you for your record only if in case something happens to me or my family in future." In the email, Shahzad said he had been called to the Inter-Services Intelligence headquarters on October 17, 2010 for a meeting with between Media Wing Director General Rear Admiral Adnan Nazir and Commodore Khalid Pervaiz, Deputy Director General of the Media Wing. Shahzad said the ISI officials had called him to discuss a report he had written two days earlier in which he said Pakistan had freed Afghan Taliban commander Mullah Abdul Ghani Baradar so that he could play a role in ‘back channel talks through the Pakistani army with Washington.’

The journalist told Nazir that the story was leaked by ‘an intelligence channel’ and that he had published it only after confirming it with a ‘most credible Taliban source’. Nazir was of the view that the report caused a lot of embarrassment for Pakistan and suggested Shahzad should issue a denial.

Shahzad wrote in his email that he had refused to comply with Nazir's demand and described it as impractical. At the end of the meeting, Shahzad quoted Nazir as saying: "I must give you a favour. We have recently arrested a terrorist and have recovered a lot of data, dairies and other material during the interrogation. The terrorist had a hit list with him. If I find your name in the list, I will certainly let you know."