Jason Tanner for The New York Times
ISLAMABAD, Pakistan — An investigative reporter for a major Pakistani newspaper was on his way home from dinner here on a recent night when men in black commando garb stopped his car, blindfolded him and drove him to a house on the outskirts of town.
There, he says, he was beaten and stripped naked. His head and eyebrows were shaved, and he was videotaped in humiliating positions by assailants who he and other journalists believe were affiliated with the country’s powerful spy agency.
At one point, while he lay face down on the floor with his hands cuffed behind him, his captors made clear why he had been singled out for punishment: for writing against the government. “If you can’t avoid rape,” one taunted him, “enjoy it.”
The reporter, Umar Cheema, 34, had written several articles for The News that were critical of the Pakistani Army in the months preceding the attack.
His ordeal was not uncommon for a journalist or politician who crossed the interests of the military and intelligence agencies, the centers of power even in the current era of civilian government, reporters and politicians said.
What makes his case different is that Mr. Cheema has spoken out about it, describing in graphic detail what happened in the early hours of Sept. 4, something rare in a country where victims who suspect that their brutal treatment was at the hands of government agents often choose, out of fear, to keep quiet.
“I have suspicions and every journalist has suspicions that all fingers point to the ISI,” Mr. Cheema said, using the acronym for the Inter-Services Intelligence agency, the institution that the C.I.A. works with closely in Pakistan to hunt militants. The ISI is an integral part of the Pakistani Army; its head, Gen. Shuja Ahmed Pasha, reports to the army chief of staff, Gen. Ashfaq Parvez Kayani.
Officials at the American Embassy said they interviewed Mr. Cheema this week, and sent a report of his account to the State Department. In response to an e-mail for comment, a spokesman for the ISI said, “They are nothing but allegations with no substance or truth.”
Mr. Cheema had won a Daniel Pearl Journalism Fellowship to train foreign journalists in 2007 and worked in The New York Times newsroom for six months at that time. He has worked at The News since 2007.
In interviews, he said his car was stopped near his home in the capital by men with the words “no fear” inscribed on their clothes. Once he was blindfolded and driven to the safe house, he was handed over to another group of men who carried out the abuse, he said. After six hours, he was dumped on a road 100 miles from the capital, Islamabad.
Mr. Cheema says he wrote more than 50 articles this year that questioned various aspects of the conduct of the military and the government, including corruption accusations against the president, Asif Ali Zardari.
But it was three articles in particular, in June, July and August, on delicate internal army problems that appear to have angered the military.
One article reported on the sensitive issue of the courts-martial of two army commandos who refused to obey orders and join the assault on a radical mosque and school in Islamabad in 2007.
The attack was believed at the time to be unpopular in the army ranks because many soldiers were reluctant to fire on fellow Muslims. Moreover, courts-martial are rarely mentioned in the Pakistani news media, and reporters have been warned not to write about them.
In his article, Mr. Cheema reported that two members of the Special Services Group, an elite commando squad, were being denied fair justice during the court-martial proceedings.
In another article, Mr. Cheema wrote that the suspects in a major terrorist attack against a bus carrying ISI employees were acquitted because of the “mishandling” of the court case by the intelligence agency.
In an article in early August, the reporter described how Army House, the residence of the chief of army staff, was protected by 400 city police officers and not by soldiers, as required by law.
In its political coverage, The News is vociferously against the civilian government of Mr. Zardari, but the opinion pages publish a cross section of views, including pro-military columnists.
While Mr. Cheema has chosen to publicize his case, he is not the only journalist or politician to come under the apparent harassment of the security services.
The law minister in Punjab Province, Rana Sanullah Khan, said that in 2003, when he was an opposition politician and had criticized the army during the presidency of Gen.Pervez Musharraf, he was kidnapped and brutalized in a similar manner.
In January, in Islamabad, the home of Azaz Syed, a reporter for Dawn, the main English-language daily, was attacked by unknown assailants days after he was threatened by supposed ISI agents over an investigative article he was researching related to the military.
Kamran Shafi, a leading columnist and himself a former army officer who writes critically of the military, was harassed and his house was attacked last December by “elements linked to the security establishment,” according to his own account.
In the last several years, journalists in the tribal areas, where the army is fighting theTaliban, have faced special risks and found it increasingly difficult to work for fear of offending either side. In September two journalists were killed in or near the tribal areas, under circumstances that remain unclear.
Pakistan has developed a rambunctious news media spearheaded by round the clock television news channels in the last decade. The military and the ISI are treated with respect by the powerful television anchors, and by newspaper reporters who extol the deeds of the army in battling the Taliban. The ISI is rarely mentioned by name but referred to as “intelligence agencies.”
One reason for the deference, according to a Pakistani intelligence official who has worked with the media cell of the ISI, is that the agency keeps many journalists on its payroll.
Unspoken rules about covering the military and its intelligence branches are eagerly enforced, Babar Sattar, a Harvard-trained lawyer, said. A journalist who trespasses over the line is told to behave, Mr. Sattar said.
Earlier this year, Mr. Cheema said he was called to a coffee shop in Islamabad by an ISI officer and warned to fall into line.
At a journalists’ seminar in Lahore, the editor of a weekly newspaper, Najam Sethi, said it was up to the ISI to declare who had attacked Mr. Cheema.
“If the ISI hasn’t done it, they should tell us who did it because they’re supposed to know,” Mr. Sethi said. “If they don’t tell, the presumption remains they did it.”
But in a column titled “Surprise Surprise” in Dawn, Mr. Shafi said, “We will never find out what happened to poor Umar Cheema because the Deep State does not want us to find out.”