"A U.S. Pathfinder ship has entered the Black Sea," the source said on condition of anonymity.
USNS Pathfinder (T-AGS 60) is an oceanographic survey ship owned by Military Sealift Command and has a civilian crew and scientists on board.
However, a Russian military source told RIA Novosti that ships of the Pathfinder class could be used for reconnaissance and intelligence gathering purposes.
"We have reliable information confirming that the [Pathfinder] ship has arrived in the Black Sea primarily to conduct intelligence gathering operations in support of the NATO naval task group currently deployed in the area," the source said.
NATO sent at least five warships, including guided missile frigates, into the Black Sea after Russia completed its operation "to force Georgia to peace" on August 12.
The operation came as a response to Georgia's attack on South Ossetia on August 8.
Another U.S. warship is expected to arrive in the Black Sea in the next few days, a Russian intelligence source said on Wednesday.
Prime Minister Vladimir Putin said on Tuesday that Russia will respond calmly to the presence of NATO warships in the Black Sea. (U.S. Coastguard cutter Dallas enters Sevastopol Harbor - Video)
"Our response will be calm, not hysterical, but there will definitely be a response," Putin said. (Russian warships arrive in Abkhazia - Video)
Meanwhile, Admiral Eduard Baltin, a former fleet commander of Russia's Black Sea Fleet, suggested last week that the NATO naval strike group currently deployed in the area could be destroyed by a single missile salvo within 20 minutes.
"Within 20 minutes the waters would be clear," he said, stressing that despite major reductions, the Black Sea Fleet still has a formidable missile arsenal.
However, Baltin said the chances of a military confrontation between NATO and Russia in the Black Sea were negligible.
"We will not strike first, and they do not look like people with suicidal tendencies," he said.