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.