The sound of grenades could be heard coming from the complex. The situation later calmed down and the gunmen lowered their weapons and could be seen walking around inside the base.
A spokesman for the Ukrainian defence ministry in Crimea Vladislav Seleznyov said on Facebook that pro-Russia militia were inside the base.
Meanwhile, hundreds of pro-Russian protesters stormed a Ukrainian air force base in western Crimea, forcing the soldiers to leave as the Ukrainian flag was taken down.
The unarmed crowd yelling “Russia! Russia!” broke through to the base in the town of Novofedorivka and started smashing windows.
Later, a Russian foreign ministry official said Russian Foreign Minister Sergei Lavrov and his US counterpart John Kerry will discuss the Ukraine crisis on the sidelines of a nuclear summit in The Hague next week.