"This is the second planned visit of Pathfinder at the invitation of Ukraine in the past 10 days," the source said.
USNS Pathfinder (T-AGS 60) is an oceanographic survey ship owned by the Military Sealift Command and has a civilian crew and scientists on board.
According to official statements, Pathfinder is searching for a ship which sank in the harbor during World War II.
The Soviet hospital ship Armenia was sunk on November 7, 1941 by German torpedo-carrying He 111 planes while the ship was evacuating refugees and wounded military and staff from Crimean hospitals. It is estimated that approximately 7,000 people died in the attack.
However, Russian intelligence believes 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.
Russian intelligence experts suspect that the ship may be carrying surveillance equipment that could survey the depths and the condition of the sea shelf and monitor the movement of submerged submarines at a distance of up to 100 km (over 60 miles).
Russia is seriously concerned over the increased presence of NATO naval forces near its main naval base in the Black Sea, which hosts at least 50 warships and smaller vessels, along with 80 aircraft.
The base has been a source of friction between Russia and Ukraine in recent years, as Ukraine's pro-Western President Viktor Yushchenko has sought NATO and EU membership for the country and demanded that the Black Sea Fleet must leave the base after a bilateral lease agreement expires in 2017.
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.
Western nations criticized Russia's counterattack as excessive and also condemned Moscow's August 26 recognition of South Ossetia and Abkhazia as independent states. Russia and NATO froze cooperation over the Georgia crisis.
Russia has blamed Western powers for encouraging Tbilisi's aggression and criticized the alliance for building up forces in the Black Sea and helping Georgia to re-arm in the conflict zone.
NATO announced on September 10 that its naval task force in the Black Sea, which consisted of Spanish, German, U.S. and Polish frigates, was leaving the region in accordance with international agreements.