Estonian Prime Minister Taavi Roivas condemned Kohver's jail term, calling it "a clear and grave violation of international law," according to BBC News.
"The staged court case that formed a verdict suitable for the Russian authorities has nothing to do with a fair trial," he said in a statement.
Estonia and the EU insist the officer was abducted on Estonian soil, while Kohver insists on his innocence.
Russia's Federal Security Sevice (FSB) said he was on a "spying operation" on Russian territory.
After his arrest for spying near the Luhamaa border checkpoint on September 5, 2014, the security official was charged with other crimes including smuggling arms and illegally crossing the Russian state border, according to Interfax news agency.
As well as the prison sentence, the court in the western Pskov region ordered him to pay a fine of 100,000 roubles (EUR 1,800).
Kohver's sentence coincided with the climax of another controversial trial, involving Ukrainian filmmaker Oleg Sentsov.
Prosecutors in Rostov-on-Don in southern Russia have called for Mr Sentsov to be jailed for 23 years, on charges of organising a terrorist group and planning terrorist attacks in Crimea.
Film-makers including Wim Wenders, Stephen Daldry, Bertrand Tavernier and Andrzej Wajda appealed on Tuesday for his immediate release, pointing out that the key witness had retracted his testimony because it was given under duress.
Estonia denies Kohver was operating as a spy and says he had been investigating smuggling operations involving Russian officials.
The dispute comes amid heightened tensions between Estonia and Russia.
In 2004, the Baltic state joined NATO and the EU. Both bodies accuse Russia of directly helping separatists in eastern Ukraine with regular troops and heavy weapons. Russia denies the claims.
In a statement, EU foreign policy chief Federica Mogherini called on Russia to release Eston Kohver, saying he had been deprived of the right to a fair trial "from the very beginning".
There was no public hearing of the case, the Estonian consul was not allowed to be present at the hearings and Kohver was deprived of adequate legal aid, she said.
Kohver is expected to be swapped for one of the Russian spies held in Estonia, according to Estonia's public radio.
