ISLAMABAD (AP) -- A Pakistani journalist who investigated al-Qaida's alleged infiltration of the country's navy was found dead Tuesday, and police said there were signs he'd been tortured.

The journalist, Syed Saleem Shahzad of the Asia Times Online, had been missing for two days. He had told a rights activist in recent months that he feared the country's intelligence agencies planned to retaliate against him over some of his reporting. Shahzad's stories on the alleged infiltration followed a deadly 18-hour militant siege of a naval base earlier last week in Karachi.

A brother-in-law identified Shahzad's body, police official Bilal Ahmad told The Associated Press. It was found roughly six miles (10 kilometers) from his vehicle in Mandi Bahauddin district outside Islamabad. An initial examination found signs of torture, but an autopsy had to be performed, Ahmad said.

Shahzad's death underscores the threats facing journalists in Pakistan, which a prominent media group said was the deadliest country for reporters in 2010. Reporters not only face pressure from militant groups but also from security agencies who operate largely outside the law.

Human Rights Watch researcher Ali Dayan Hasan said that the 40-year-old Shahzad had told him he feared that the spy agencies were after him, and that he had received a veiled threat in a meeting with a navy officer at the headquarters of Pakistan's Inter-Services Intelligence agency in October.

Shahzad forwarded notes from that meeting to Hasan, saying in an email that it was for the "record only if in case something happens to me or my family in future." The rights activist also said he was told by some Pakistani government officials that they believed Shahzad was in ISI custody.

A senior Pakistani intelligence official denied allegations that the agency had anything to do with Shahzad's case.

"It's absurd," the official told The Associated Press on condition of anonymity because he was not authorized to speak to media on the record.

The siege of the naval base was deeply embarrassing to a security establishment that was already reeling from the unilateral U.S. raid that killed Osama bin Laden in northwest Pakistan. Pakistan has protested the incursion as a violation of its sovereignty.

Asia Times Online is a Hong Kong-based news Website with more than 50 correspondents and contributors in 25 Asian countries, the U.S. and Europe. Shahzad, a married father of three who was originally from Karachi, is believed to have worked for other news agencies also, including one based in Italy.

The Committee to Protect Journalists says that Pakistan was the deadliest country for journalists in 2010, with at least eight media workers killed in the line of duty. Six of the journalists in Pakistan were killed in suicide attacks, the group said.

The Pakistan Federal Union of Journalists strongly condemned Shahzad's killing, and demanded a high-level investigation.

"This is tragic," said Amin Yousuf, secretary-general of the union. "We are losing our professional colleagues but the government never unearths who is behind the killing of journalists."

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Associated Press writers Zarar Khan, Asif Shahzad and Chris Brummitt contributed to this report.