The second man will stand trial for murder, RIA Novosti reported.
Authorities said the two men and two of their friends disappeared while fishing in Yakutia in August 2012. The two survivors were found in late November 2012 and told investigators that they had no idea what happened to their companions.
However, later, the skeletal remains of one of the other men were discovered not far from where the survivors were rescued. Investigators said the body had been hacked into pieces with an axe and had little flesh remaining on them.
Yakutia's branch of the Russian Investigative Committee said in a statement one of the survivors allegedly smashed the deceased's head with an unknown object.
"Investigators have established that the suspect and his friend dismembered the dead body and ate it because they had no other food," the committee said.
The fate of the fourth man is unknown.
The man accused of killing his companion is being held on murder charges. The other man has been cleared of charges because there was no evidence of his involvement in the killing and Russia does not have laws on cannibalism.
The names of the survivors and the other two men were not reported.