Lieutenant Sergei Lapin of the Russian interior ministry's special forces unit OMON was sentenced in Grozny to 11 years in prison for the illegal arrest, torture and disappearance of 22-year-old Zamil Khan Murdalov in 2001.
Lapin's lawyer said he would appeal the court's decision, while Murdalov's family said they felt the sentence was too light.
Chechen human rights organisations expressed concerns that Lapin might be surreptitiously freed in a few years.
The ruling is "illegal, has no validity, is not motivated in any way, not proven.... I did not expect anything else," Lapin told Russian television channel NTV after the verdict.
The trial, which started in September 2003, was the first of its kind held in Chechnya, where many alleged crimes committed by Russian soldiers and pro-Moscow forces go unpunished.
"The fact that the trial and the verdict took place in the Chechen republic is above all a sign ... that the people live under the protection of the Russian constitution," pro-Moscow Chechen Deputy Prime Minister Ramzan Kadyrov said.
According to a human rights organisation, Memorial, an estimated 3000 to 5000 people have gone missing since Russian troops invaded the region in 1999.