Igor Sutyagin was accused of passing sensitive information on Russian nuclear submarines to U.S. intelligence, ITAR-Tass reported.
The high court ruling came in a re-examination of Sutyagin's case as a result of a ruling by the European Court of Human Rights that found Russia violated Sutyagin's rights to a fair trial and ordered compensation of $25,000.
Russia pardoned and released Sutyagin under a spy exchange deal with the United States in 2010, RIA Novosti reported.
He and three other prisoners were released in exchange for 10 people accused by the United States of spying for Russia, including Anna Chapman.
Sutyagin, currently residing in London, refused to participate in the Russian Supreme Court review of his case.
He has said he wants to return to Russia to be with his family but has been warned by his friends not to do so.