ISLAMABAD, Pakistan — Pakistan’s top spy agency, the Inter-Services Intelligence directorate, issued an unusual public statement Wednesday in which it denied involvement in the killing of a Pakistani investigative journalist who was found dead Tuesday.

 Syed Saleem Shahzad, 40, whose work focused on security and militancy, disappeared from this capital city Sunday evening. Other journalists and human rights activists quickly suspected he had been abducted by Pakistani intelligence services.

The bureau chief of the Hong Kong-based Web site Asia Times Online, Shahzad told colleagues he had received several warnings about his work from those agencies, including as recently as October. At that time, Shahzad told a human rights activist in an e-mail, ISI officials summoned him for a meeting in which they issued what he considered an oblique threat to his life.

The ISI statement, issued in the form of an article published by the state press agency, condemned Shahzad’s death and said that October meeting “had nothing sinister about it.” The agenda of the meetings like that one, the statement said, is to provide “accurate information on matters of national security” and notify people about any threats to their lives.

 “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 said, noting that Shahzad’s e-mail had also described the meeting as “extremely polite and friendly.” 

 Days before his death, Shahzad published an article that said Pakistani naval officials had been talking with al-Qaeda about the possible release of its members who had formed a cell within the navy. Following the breakdown of discussions, al-Qaeda carried out last week’s attack on a Pakistani naval air base in Karachi, he reported.

 The ISI is Pakistan’s main military intelligence agency, and U.S. officials accuse it of aiding militant organizations that strike in India and against coalition forces in Afghanistan. The agency is widely believed in Pakistan — and by international human rights organizations — to also intimidate and sometimes detain militants, journalists, activists and politicians. Human rights activists say those detentions sometimes lead to torture or death.

The agency faced rare criticism in Pakistan during the past month, mostly over its failure to detect Osama bin Laden, who lived for five years in a military garrison city. Like many lawmakers in Washington, some Pakistani commentators accused the ISI of harboring bin Laden.

Soon after his disappearance, Human Rights Watch said it had been told by “credible sources” that they believed Shahzad was in the custody of intelligence services.

 On Wednesday, the ISI accused the media of using Shahzad’s death for “targeting and maligning” the agency, and it said it would help bring the killers to justice.