Kohver, who was sentenced in August to 15 years in jail on espionage and other charges, was exchanged for Aleksei Dressen, a former Estonian security official serving a 16 year sentence for spying for Moscow, the FSB security service said.
"On September 26, Estonian special service officer Eston Kohver, who was convicted in Russia for espionage, was exchanged for Aleksei Dressen, a former officer of Estonia's security police, who has been serving a sentence for giving secret data to the Russian FSB," said a statement carried by Russian news agencies.
Kohver's defence lawyer Mark Feigin said the swap was "organised on the political level" and was timed to boost Russia's image ahead of President Vladimir Putin's speech at the United Nations on Monday.
"It's all happening ahead of Putin's visit to the UN tomorrow. There are no other reasons," Feigin wrote on Twitter.
Dressen was convicted in 2012 together with his wife Victoria, who was given a suspended sentence. He was found guilty of treason for funnelling classified information to Russia for years after Estonia's 1991 independence.
The scandal was the latest in a series of spy cases involving Russia and the Baltic states, former Soviet republics turned NATO and EU members increasingly wary of Russia's intentions following the annexation of Crimea from Ukraine in 2014.
Russia's relations with the West have hit their lowest point since the Cold War over the conflict in Ukraine, leading to a spike in spying claims.
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