"Our records indicate that over 2,800 people disappeared in 2000-2007, and 1,500 disappeared in 1994-1996," Nurdi Nukhazhiyev told a news conference.
Chechnya, with a population of over a million people as of 2002, was devastated by two military campaigns, in 1994-1996 and 1999-2001. In recent years, Moscow has substantially scaled down its military presence.
However, gunfights and terrorist attacks still occur in the area, despite a widely publicized amnesty for gunmen announced by Russian authorities.
Russian authorities have been criticized by the West for alleged human rights violations in Chechnya.
The European Court of Human Rights in Strasbourg ruled in April that Russia must pay a Chechen woman about $70,000 in compensation for moral damages related to her husband's disappearance and alleged killing in 2000.
Some 200 similar cases are currently pending before the Strasbourg Court.
The Chechen human rights chief said: "These [missing] people disappeared without a trace during the so-called mopping-up operations at military checkpoints, rather than during combat action."
Nukhazhiyev also said many mass graves had been found in Chechnya, which might hold over 3,000 unidentified remains of military personnel and civilians, including those considered missing.
The official said Chechen authorities had allocated 47 million rubles (about $1.8 million) to set up a lab that would help identify the discovered remains, but were waiting for special equipment promised by the Council of Europe in 2005.
