"Talks on the presence and function of Russia's Black Sea Fleet, as well as disputes over the Kerch Strait, will be held in Kiev in late September," Andrei Nesterenko said.
Russia is set to leave the Sevastopol base when the current lease agreement expires in 2017. 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.
Russia has accused Kiev of pursuing "unfriendly" policies over the Black Sea Fleet base.
Yushchenko has called for the Russian navy's early pullout, tougher deployment requirements and higher fees, demands that have not been backed by his former coalition ally, Prime Minister Yulia Tymoshenko.
Russia-Ukraine tensions heightened after several Black Sea Fleet warships dropped anchor off the Georgian coast during and after last month's armed conflict with Tbilisi over breakaway South Ossetia.
Russia's naval base in the Crimea currently has 50 warships and patrol boats, along with around 80 aircraft, and employs coastal defense troops.
The two countries are also in a dispute over a maritime boundary in the Sea of Azov. Ukraine insists that a state border be drawn in the Kerch Strait that completely coincides with the administrative border that existed in the former Soviet Union.
Russia maintains that inland water areas were not delimited between the former Soviet republics and therefore, this principle is not applicable.