Russia has ordered its naval commanders to negotiate the return of a lighthouse in the Crimea which it says was seized by Ukrainian officials on Friday.
Moscow says the lighthouse, claimed by Kiev as its property, is crucial for the safety of its Black Sea fleet.
The two countries struck a deal in 1997 on the division of the Soviet Black Sea fleet and the lease of Ukrainian facilities by the Russian Navy.
Kiev officials have suggested charging Russia more rent for Black Sea bases.
The latest row comes barely two weeks after Moscow and Kiev resolved a bitter dispute over gas prices after Ukraine was forced to accept higher prices for Russian gas.
Tensions over the Black Sea fleet have been simmering for many months but now appear to be escalating, says the BBC's Helen Fawkes in Kiev.
The Russian navy claims to have foiled an attempt on Saturday to occupy another lighthouse in the Crimea.
It comes after Moscow accused Ukraine of seizing a lighthouse in the Crimean city of Yalta on Friday during a maintenance trip.
Despite the war of words, Russian naval commander-in-chief Vladimir Masorin seemed keen on Saturday to use negotiation to resolve the dispute.
"The position of the Russian naval headquarters is firm: the Yalta lighthouse must be returned to Russian hydrography services," he was quoted by Russian news agency Interfax as saying.
"I have given the order to the commander of the Black Sea fleet to take back control of the lighthouse, by use of methods of civilized discussion."
'No legal basis'
The Ukrainian foreign ministry says the Russia's claims Kiev "seized" the lighthouse are deliberate misinformation.
"You can't seize something that's yours," Foreign Minister Boris Tarasyuk told Interfax. "There is no legal basis for Russia to insist that these sites are part of the Black Sea fleet."
His ministry claims that all hydro-graphic sites and navigation equipment on the Crimean coast, including the Yalta lighthouse, are the property of Ukraine.
A spokesman told reporters that Russia currently "unlawfully" controls 35 of the 100 hydro-graphic sites in Crimea.
The Ukrainian foreign ministry has previously accused the Russian Black Sea fleets of violating the conditions of their long-standing agreement by refusing to hand over navigational facilities.