Russia and Estonia have exchanged two men accused of espionage at a remote border post at a time of heightened tensions between the neighbours.

Russia's Federal Security Service (FSB) said on Saturday that it handed over Eston Kohver, an Estonian security officer detained by Russia last year, in exchange for Alexei Dressen, a former Estonian official serving a 16-year prison term for being a Russian spy in 2012.

Estonian officials confirmed the swap, which took place at a bridge over the Piusa River in a forested border region located a few kilometres south of Lake Peipus.

Russian state television showed a seemingly casual exchange with two men, each with one companion, meeting at the middle of a bridge, briefly embracing the handlers and walking off.

"I am very happy to be back in my homeland. I would like to thank all those to whom my welfare was important, everyone who supported me. I would particularly like to thank the people who helped my family cope when I was gone," Kohver said, during a news conference following his release.

'Long negotiations'

Kohver's arrest last September provoked a dispute between the two countries. Estonia said he was abducted on the Estonian side of the frontier, but Russia said he had been caught on its territory carrying a pistol and ammunition, 5,000 euros in cash and spying equipment.

"There were negotiations, long negotiations, between institutions, and the conclusion was that there would be an exchange," Estonian Interior Minister Hanno Pevkur told journalists after welcoming Kohver back home.

Dressen, the alleged Russian spy, was detained at the airport in the Estonian capital Tallinn with his wife in February 2012, just before she was due to board a flight to Moscow, carrying what Estonian prosecutors said were classified documents.

Russian news agency RIA cited a source in the FSB as saying Dressen had worked for Russian counter-intelligence since the 1990s, transferring information about US and British spies working in the Baltic countries.

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.

Source: Agencies