10:00 AM update to TIME report I cited below:
Pakistan's main news channels are reporting that Shahzad's dead body has been found. One news channel broadcast what appeared to be a black and white image of Shahzad's face. There were visible signs of torture.Asia Times Online is also reporting that Shahzad's body has been found by police and that it bears marks of torture.
Missing Pakistani journalist Syed Saleem Shahzad
with Giuseppe Marra, chief of AdnKronos International news agency
with Giuseppe Marra, chief of AdnKronos International news agency
The Asia Times Online still hasn't commented on their bureau chief's disappearance; a note on the website says that due to the holiday they won't be uploading reports until May 31; perhaps the uploaders are still getting their beauty sleep because the uploads aren't there yet.
Ifnan Khan at Pakistan's Daily Times got the scoop by several hours on the news that Human Rights Watch (HRW) has, through "credible sources," learned Shahzad is in the custody of the Inter-Services Intelligence (ISI). But I'm going to run with the report from TIME, which has much more detail and background than the Daily Times report. See TIME's website for source links in the report:
A Pakistani Journalist Vanishes: Is the I.S.I. Involved?The International Federation of Journalists has also issued an appeal to Pakistan's government on Shahzad's behalf (press release via New Zealand Scoop news site:
By Omar Waraich
Islamabad; Tuesday, May 31, 2011
Fears are growing for the safety of a well-known Pakistani journalist who has been missing for 39 hours now and, according to an international advocacy group, is believed to be in the custody of the Pakistan's controversial Directorate for Inter-Services Intelligence (ISI). Human Rights Watch declared that Saleem Shahzad, a reporter working for the Hong Kong-based Asia Times Online and Adnkronos International, the Italian news agency, could be subject to mistreatment and even torture while in custody.
While the ISI was said to have bristled at previous reports by Shahzad, his disappearance happened two days after he wrote a story for Asia Times Online that said that al-Qaeda had attacked a naval base in the port city of Karachi on May 22 after talks had broken down between the Pakistan navy and the global terror organization. In his report, Shahzad claimed that al-Qaeda had carried out the attack in retaliation for the arrest of naval officials suspected of links with the terror group.
The 17-hour attack on the Karachi naval base by at least four attackers led to the destruction of two Lockheed Martin P-3C Orion aircraft that had been enhanced with counterterrorism capabilities. An investigation is currently underway. At the time of the attack, former military officers and analysts speculated that it could not have been mounted without some help from the inside.
On Monday, Pakistani intelligence officials told journalists that they had picked up Kamran Ahmed Malik, a former navy commando, in Lahore on Friday. Malik and his brother have been detained in connection with the investigation. While Malik has not been formally charged, it is widely reported that he is being held for questioning about his links to both the terrorists and former colleagues inside the Navy.
Shahzad, the missing journalist, is believed to have been abducted by intelligence agents from the well-heeled F-6/2 area of Islamabad at around 5:45 p.m. At the time, he was on his way to the studios of Pakistan's Dunya News channel to discuss the contents of his latest report about the naval base attack. He had driven there from his house in central Islamabad's leafy F-8/4 neighborhood, some four kilometers away. At quarter to six, Shahzad had responded to a call from a producer at Dunya News and said that he was on his way, says Nasim Zehra, director of current affairs at the channel. No one has heard from him since.
The following morning, Ali Dayan Hasan, a senior researcher at Human Rights Watch, received a call from Shahzad's wife.
"He had told her that I was one of the people that should be called in case anything happens to him," says Hasan.
"He had feared for sometime that something like this would happen to him."
Later, Human Rights Watch was able to establish that Shahzad was being held by the ISI.
"We were informed through reliable interlocutors that he was detained by the ISI," says Hasan.
Those interlocutors, he adds, had received direct confirmation from the agency that it was detaining Shahzad. In any case, Hasan says, "in a high security zone like Islamabad, it is only the ISI that can effect the disappearance of man and his car without a trace."
Human Rights Watch was also told that Shahzad was supposed to return home on Monday night.
"The relevant people were informed that his telephone would be switched on first, enabling him to communicate with his family," says Hasan.
"They were told that he would return home soon after."
But by 1 a.m. on Tuesday morning, Shahzad had still not been heard from. At that point, Hasan recalled that Shahzad had sent him an email on Oct. 18, 2010 that was to be released in the event of his disappearance. At the time, says Hasan, he was "fairly sure that sooner or later something was going to happen."
Human Rights Watch says that it has made repeated attempts to contact the Pakistan government and establish Shahzad's whereabouts, but has received no response.
On Oct. 17, Shahzad had been summoned to the ISI's headquarters to discuss the contents of an article published the day before with two officials from the agency's media wing. That report, published in Asia Times Online, alleged that Pakistan had quietly released Afghan Taliban commander Mullah Baradar, Mullah Omar's deputy, to take part in talks through the Pakistan Army.
According to the email, labeled "For future reference" and seen by TIME, one of the officials said the following words to Shahzad: "I must give you a favor. We have recently arrested a terrorist and recovered a lot of data, diaries and other material during the interrogation. The terrorist had a list with him. If I find your name in the list, I will certainly let you know."
Incidentally, the two ISI officials present at the meeting, Rear Admiral Adnan Nawaz and Commodore Khalid Pervaiz, are both from the Navy. Pervaiz has just been appointed the new commander of the Karachi naval base that was attacked.
Hasan of Human Rights Watch says that statement can be read as a threat. "The tone and the manner in which it was issued did constitute a threat," he says. "Shahzad described it to me."
The rest of the meeting, as Shahzad described it in the email, was held in "an extremely polite and friendly atmosphere," but no words were minced. In the email, the ISI official was said to have asked for the source of his story. Shahzad writes that he would not name the source, but said that he had been told the information by an intelligence official and later confirmed the story from "the most credible Taliban source." According to Shahzad's account, he was asked to "write a denial of the story" but "refused to comply with the [ISI] demand."
Many of Shahzad's media colleagues speculate that the ISI is holding him to extract the identities of his sources. "It is very difficult to say what they want from him," says Hasan.
"But when the ISI picks up journalists in this manner, they are often subjected to mistreatment and torture. The longer he stays in their custody, the greater the likelihood is that he will be tortured."
Last September, Umar Cheema, an investigative reporter for The News, an influential Pakistani daily, was kidnapped, blindfolded, stripped naked, had his head and eyebrows shaved, beaten, filmed in humiliating positions, and dumped on the side of the road six hours later.
"If you can't avoid rape," one of his interrogators jeered during the ordeal, "enjoy it."
The perpetrators were never found, but when asked about his suspicions, Cheema told the New York Times: "I have suspicions and every journalist has suspicions that all fingers point to the ISI."
The disappearance of Shahzad is a reminder of the multiple hazards faced by journalists working in Pakistan. In January, Wali Khan Babar, a respected reporter for Geo News, was gunned down in Karachi. 
Last month, reporter Abdullah Bhittani cheated death after being shot three times in Rawalpindi, while a radio station in the northwest town of Charsadda was bombed. Bhittani has recovered, but with 10 slain journalists last year, the Washington DC-based Newseum called Pakistan "the deadliest country in the world for journalists." Reporters Without Borders ranked it 151st out of 178 countries when it comes to press freedom.
The principal threats, human rights campaigners say, come from military intelligence agencies and Islamist militants.
"As a consequence, it is becoming difficult for journalists to perform their basic professional duties in the context of a war between the Pakistani state and the militants," Hasan says.
"Both parties target journalists, arbitrarily and with brutality."
Human Rights Watch has called on the Pakistan government to locate Shahzad, return him safely to his home, and hold those who held him "illegally" accountable. "To date, no intelligence personnel have been held accountable for frequently perpetrated abuses against journalists," laments Hasan. "Tolerance for these practices has to end, now."
Tuesday, 31 May 2011, 3:11 pmSee Shahzad's website for more information about him.
Press Release: International Federation of Journalists
Appeal to Pakistan Government to Find Missing Journalist
May 31, 2011 - The International Federation of Journalists (IFJ) urgently appeals to the Government of Pakistan to order its security and police agencies to respond immediately to find a senior journalist who disappeared in Islamabad on May 29.
Syed Saleem Shahzad, the Pakistan bureau chief for Asia Times Online , went missing in the early evening [around 5 PM Pakistan time] while heading to the office of Dunya TV [a private TV station] to record a program.
The IFJ and its affiliate, the Pakistan Federal Union of Journalists (PFUJ), hold grave fears for the welfare of Shahzad, who published the first of a two-part investigative series into alleged links between Al-Qaeda and Pakistani naval officials on Asia Times Online on May 26.
“The IFJ is deeply worried for the safety of Syed Saleem Shahzad,” IFJ Asia -Pacific Director Jacqueline Park said.
“We appeal as a matter of urgency for Pakistan ’s Government to do all it can to find Shahzad quickly, and to prove a commitment to reverse Pakistan ’s poor track record in investigating abuses against journalists.”
Regarding the controversy generated by his most recent investigative report for Asia Times Online, which is supposed to be a two-parter (the second part hasn't been published yet), his May 27 report opened with this paragraph
Al-Qaeda carried out the brazen attack on PNS Mehran naval air station in Karachi on May 22 after talks failed between the navy and al-Qaeda over the release of naval officials arrested on suspicion of al-Qaeda links ...Pakistan's regime had chalked up the attack to the so-called Taliban, and a so-called Taliban group had claimed responsibility for it.
As to how much stock I'm putting in Shahzad's report, I've discussed this kind of question before. He belongs to that category of reporter who specializes in cultivating high-level sources in civilian government/military, many of which are anonymous. (In this case, sources in Pakistan's regime.)
Such sources are a double-edged sword: very useful for gaining inside information but they can also use the reporter as a conduit; i.e., to get into the public domain a point of view among a particular faction in government/military for reasons that are not always clear to the public -- or the reporter. So such reportage is a high-wire act, both for the reporter and the news consumer.
Right now I'm reading Shahzad's report as pieces of a large jigsaw puzzle called 'the present thinking inside Pakistan's military.' But my overriding concern at this time is his safety. Shahzad also cultivated sources among terrorist groups. HRW could have been misled by the informant, or the informant could have been misled. Pea-soup fog.
1) Sultan Hijazi, a TIME reader, asserted in the report's comment section "Wali Khan Babar was killed by his colleague at Geo News; the author should get his facts right." I have not followed the issue and so have no idea whether Hijazi is correct.