Pakistan: ISI denies role in journalist Syed Saleem Shahzad’s death (VIDEO)

Pakistan's spy agency, the Inter-Services Intelligence (ISI) directorate, issued a rare public statement Wednesday denying involvement in the killing of Pakistani journalist Syed Saleem Shahzad, who was found dead Tuesday.

Shahzad, 40, was a well-known journalist who worked as the Pakistan bureau chief of the Hong Kong-based Asia Times Online and wrote for the Italian news agency Adnkronos International.

He covered security and terrorism issues and days before his death wrote about the alleged infiltration of Al Qaeda into Pakistan's navy, claiming that the 15-hour assault by militants on a naval base in Karachi on May 23 was a revenge attack for the arrest of naval officials because of their suspected links with Al Qaeda.

Shahzad disappeared Sunday and many journalists and human rights activists suspected he had been taken by Pakistani intelligence services.

After his death, many accused the ISI of involvement, citing Shahzad's earlier warnings to Human Rights Watch researcher Ali Dayan Hasan that he had been threatened by the spy agency. Shahzad sent Hasan an email in October informing him that he had been threatened by the ISI, Pakistan's main military intelligence agency.

In a statement published in the state press, the ISI Wednesday insisted its meeting with Shahzad in October “had nothing sinister about it," the Washington Post reports. Instead, it was merely an effort to provide “accurate information on matters of national security” and warn people about possible threats to their security.

“The reported e-mail … which is being made the basis of baseless allegations leveled against ISI has no veiled or unveiled threats in it," the statement read.

The ISI has long been accused by Pakistani and international rights groups of intimidating and sometimes detaining militants, journalists and activists, the Washington Post states.

At least 16 journalists have been killed in Pakistan since 2002.

An editorial in the New York Times calls on the ISI to "pledge a robust and transparent hunt for whoever was responsible" for Shahzad's death.

"They must make clear to all who work for them that they will not tolerate attempts to silence reporters or anyone who dares to raise questions," it states.

The ISI has already been under criticism after a U.S. raid found and killed Osama bin Laden in Abbottabad, Pakistan, on May 2.

Meanwhile, autopsy results of Shahzad showed that the journalist had at least 15 torture marks on his body but no bullet wounds, the Times of India reports.

It showed he likely died as a result of a fatal blow in the chest region.

"It was an attempt to silence a society," Adil Najam, a professor of International Relations and Geography in Boston University, told the Times of India.

Hundreds turned out for his burial in Karachi. See the video below.