The defendants, who pleaded not guilty, were also stripped of their commissioned ranks, however, only Sergei Arakcheyev appeared in court as Khudyakov failed to turn up, his lawyer said she had no idea of his whereabouts.
The Supreme Court previously overturned a jury's not guilty verdict against the defendants following a Constitutional Court ruling that serious crimes committed in Chechnya should be heard by a military court rather than a trial by jury.
Khudyakov and Arakcheyev were charged with the murders of three construction workers in the Chechen capital, Grozny, in January 2003.
The prosecution demanded 18- and 20-year prison sentences, respectively, for Khudyakov and Arakcheyev. Defense representatives said they would appeal the verdict.
Representatives of the victims said they were satisfied with the verdict, as their main aim was that the officers should be found guilty of the murders.
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