Being a journalist, I’m always in search of a juicy story. Last month I happened on one I’ll remember forever: a torture operation conducted presumably by thugs of Pakistan’s intelligence agency under the nose of the federal government in Islamabad. Unfortunately, I was the central character.

On Sept. 4, I was heading home late at night from dinner with friends when a group of 10-12 men stopped my car. They were wearing commando fatigues, and the words “No fear” were inscribed on their shirts. They seized me, cuffing my hands and muffling my head and face as if I was some high-value al Qaeda leader. Then they drove me to a secret place where they stripped me naked, put me face-down on the floor, and tied my hands behind my back. Breathing was hard since my face was so tightly wrapped.

Soon after, my captors started lashing my naked body with a long piece of leather and a wooden rod. I was not aware of my crime until I was told during the beating: “This is the consequence of writing against the government,” they said as they whipped me. The language these thugs used to address me was filthy—they sounded like they were living in medieval times, treating fellow citizens as their subjects.

The physical torture lasted almost half an hour, leaving me in excruciating pain. Shaving my head and eyebrows followed. Next, they took my picture in different humiliating poses.

Six hours later, I was dumped 120 kilometers outside Islamabad with a warning: “If you tell the media about this, you’ll be abducted again—and won’t ever be returned. And your nude pictures will be put on YouTube.”

Ten minutes after I was released, I made the decision to speak up regardless of the consequences. My convictions can’t be stamped out with torture, I told myself. And this was not the first attempt: I was also targeted in December 2004 when a car hit me twice, leaving me with a compound fracture in my left leg that kept me bed-ridden for six months.

I cannot live without freedom. It is worth any price—even my life. People ask me what lesson I’ve learned from this terrible episode. I say it has given me a new reason to live.

Instead of submitting to fear, I’ve decided to form a coalition of Pakistani journalists committed to waging a public struggle against such efforts to repress our freedom. We’re also setting up the Center for Training and Investigative Reporting to cultivate a new crop of reporters who will continue our important work.

I was not the first to be tortured by such thugs, but I am the first to speak out so publicly and expose myself to more serious risks. The news about my ordeal was on television within hours, triggering anger and country-wide condemnation. The Pakistani government ordered an immediate inquiry into the incident.

Who is responsible for this barbaric act is still hotly debated. But the most prominent journalists and politicians in the country believe that the Inter-Services Intelligence (ISI)—the army-controlled intelligence agency, Pakistan’s equivalent of the CIA—carried it out.

There are many reasons we suspect the ISI. For years, I have written investigative reports criticizing the army, the intelligence agencies and the government. But only the people from the ISI would approach me, directly or indirectly, when my stories were published. The spy agency has a history of sorting out its critics whether they are journalists, politicians or ordinary citizens.

Regardless of who committed this crime, the culprits must be brought to justice. In the current culture, killing a journalist is not a big deal. So far in 2009-2010, 23 journalists have been killed and 45 have been wounded, according to the Pakistan Federal Union of Journalists.

Yet in the past few decades no murder case of a journalist has reached the stage of prosecution, according to the Committee to Protect Journalists. The only exception is the case of Daniel Pearl, the Wall Street Journal reporter who was abducted in January 2002 and beheaded a month later in Karachi. Incidentally, I was a Daniel Pearl Journalism fellow at the New York Times in 2008.

Though a government body is conducting a probe of my case, if history is any guide the investigation will reach a dead end and the elements who seek to silence us will be emboldened. I strongly appeal to the community of journalists world-wide, to the World Editors Forum and other organizations, to stand with us in this time of crisis. The outcome of my case is critical to the fate of all journalists in Pakistan and beyond.

Mr. Cheema is an investigative reporter for the largest English-language Pakistani newspaper, The News.