The Italian, a captain of a frigate, and the Russian, a military official accredited at the embassy, were accused of "serious crimes tied to spying and state security" after their meeting on Tuesday night, Italian police said. The suspects were not identified.
The Italian foreign ministry said it had summoned Russian ambassador Sergey Razov following the arrests. Russia's RIA news agency quoted the Russian embassy as saying it hoped the incident would not affect bilateral relations.
The incident was the latest in a series of spying accusations in recent months against Russians in European countries. Bulgaria expelled Russian officials on suspicion of spying in March, and the Netherlands did so in December.
The arrests were ordered by Rome prosecutors following a long investigation carried out by the Italian intelligence with the support of the military, the Carabinieri police force said.
The Italian official was taken into custody, while the position of the Russian was still under consideration in view of his diplomatic status, the police added.