Guards came across two unidentified persons breaking into a weapons depot near Chernomorskoye, western Crimea, early Tuesday morning, a statement said.
The two escaped, but guards then discovered a depot with a forced padlock from which two missiles stored in containers and a launch system for the Strela-3M portable air defence missile system were missing.
Police were searching for the thieves and a special commission headed by the deputy head of Ukraine's navy, Igor Matviyenko, had gone to the scene to investigate, the defence ministry said.