Tallinn has accused Moscow of abducting Eston Kohver at gunpoint from Estonian territory. He now faces up to two decades in jail.
The arrest of the Estonian national came just days after US President Barack Obama visited the former Soviet state last week to calm the nerves of Washington's Baltic allies over the Ukraine crisis.
"Eston Kohver was charged on September 8 with espionage," his lawyer Nikolai Polozov told AFP today. "He faces up to 20 years in prison."
Along with fellow Baltic states the nation of 1.3 million joined the EU and NATO in 2004 as a bulwark against Russian influence.
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Polozov said that he had not yet been able to visit Kohver, who is being held in Moscow's Lefortovo prison, used to jail those being investigated by the FSB security services.
"I can't yet give his version of events since my colleague and I only took on the case yesterday and so far have not managed to see our client," Polozov said.
The FSB, the successor agency to the Soviet-era KGB, declined immediate comment on Thursday.
In a rare public statement, the FSB announced last week it had detained Kohver as he attempted to carry out intelligence gathering in northwestern Russia close to the Estonian border.