Valentin Danilov was arrested in 2001 on charges of passing classified information on space technology to China. He claimed the information was already publicly available.
He was acquitted in a 2003 trial, but retried the next year and convicted and sentenced to 14 years.
After his release Saturday, Danilov told a news conference in the Siberian city of Krasnoyarsk that he would pursue his case with the European Court of Human Rights.
"Nobody still has told me what kind of secrets I have," Danilov said Saturday.
Danilov, who was a professor at Krasnoyarsk Technical University, was one of several Russian scholars and journalists prosecuted for alleged espionage by the Federal Security Service, the main KGB successor known under its Russian acronym FSB.
Rights advocates say the security agency has been emboldened in efforts to discourage Russians' unsupervised contacts with foreigners since Vladimir Putin, a former KGB officer and FSB head, became president.
Danilov's release came 10 days after a new law went into force that broadens the definition of treason and which critics say could be used against politically inconvenient figures.
While the previous law described high treason as espionage or other assistance to a foreign state that damages Russia's external security, the new legislation expands the definition by dropping the word "external." Activities that fall under it include providing help or advice to a foreign state or giving information to an international or foreign organization.
Danilov said after his release that "I'll continue to be involved with science, but not connected with space, because everything that's connected with space, everywhere it's a state secret."