Hundreds of people are mourning the death of a Pakistani journalist, as the country's spy agency denies involvement in his torture and killing.

Syed Saleem Shahzad was buried in Pakistan's southern port city of Karachi on Wednesday, as relatives, journalists and local politicians looked on.

Shahzad's body was found about 200 kilometers from Islamabad on Tuesday, after he was reported missing earlier this week. Police say it showed signs of torture.

The 40-year old father of three worked for the Hong-Kong based Asia Times Online and other publications. After last weeks' brazen militant attack on a Pakistani naval base he had written an article in which he alleged al-Qaida had links with the Pakistani navy.

A Human Rights Watch researcher, Ali Dayan Hasan, said Shahzad had told him that he feared Pakistani intelligence agents were after him.

On Wednesday, an unnamed official with Pakistan's Inter-Services Intelligence agency said allegations that the spy agency had threatened Shahzad or was somehow involved in his murder were “baseless” and” unfounded.”

The ISI official told the Associated Press of Pakistan that the journalist met with ISI officials in October of last year to discuss a story Shahzad had written and that the meeting was “polite” and “friendly.” The intelligence official added that Shahzad's death should not be used to target and malign the country's security agency.

Interior Minister Rehman Malik has announced a police investigation into Shahzad's killing.

Dozens of journalists took to the streets throughout Pakistani cities on Wednesday to protest Shahzad's death. The journalists' union also declared two days of mourning.

Pakistani Prime Minister Yusuf Raza Gilani has expressed regret over Shahzad's death and ordered an immediate investigation.

Human rights group Amnesty International says any probe into Shahzad's abduction and death must investigate whether Pakistan's security and intelligence agencies, especially the ISI, was involved.

Amnesty's Asia-Pacific Director, Sam Zarifi, said Tuesday that Pakistan's intelligence agencies face serious allegations that they have been involved in the numerous killings of activists, lawyers and journalists.

U.S. Secretary of State Hillary Clinton also strongly condemned Shahzad's killing and welcomed Pakistan's probe. She said the journalist's reporting on terrorism and intelligence issues exposed the troubles extremism poses to Pakistan's stability.

Shahzad was last seen leaving his home in Islamabad on Sunday to participate in a television interview.