Alexander Tugushev, a former deputy head of the State Fisheries Committee, and three other defendants faced charges of extorting $3.7 million from the management of a fishing company based in the Pacific port of Petropavlovsk-Kamchatsky to issue illegal fishing quotas in 2003.
However, Moscow's Tverskoi District Court cleared Tugushev of bribery charges.
"The court came to a decision that Tugushev is guilty of extortion, particularly of embezzlement on a large scale," the court said in a verdict.
The other defendants, who have also been in custody since August 2005 on suspicion of acting as middlemen in the scheme, have been sentenced to five and half years in prison.
The court also ruled that the convicts pay $3.63 million to the company at the center of the scandal.