Speaking at a human rights conference rounding up his three-day visit to Chechnya, Thomas Hammarberg said prisoners had told him they were regularly tortured and brutally treated.
Hammarberg called for measures to be taken to punish the culprits, including surprise checks during interrogations to prevent torture and forced confessions, which, he said, destroy the entire justice system.
The commissioner said the Council of Europe was ready to help find those to blame and those who have gone missing in Chechnya, which has been devastated by two military campaigns in 1994-1996 and 1999-2001. He said the efforts might involve the exhumation of bodies.
The European official, however, warned of possible political obstacles, and added he would raise the issue during his visit to Moscow Friday.
Following an official ending of the military campaign in Chechnya in 2001, Moscow has significantly scaled down its military presence in the republic, but random fighting and terrorist attacks still occur in the area spilling over to neighboring regions.
President Vladimir Putin nominated Thursday ex-premier and acting Chechen president, Ramzan Kadyrov, to the Chechen presidency. Former militants, the Kadyrovs switched sides helping federal troops crush insurgency. Kadyrov still has a private army, which helps maintain order but has also been accused of kidnappings and other crimes by human rights groups.