The ministry said an officer and a soldier were seized by "extremists" yesterday and taken to an unknown destination after they pulled over to repair their vehicle.
It said several branches of Ukraine's armed forces were involved in a search for the missing soldiers, and vowed a "firm response" against those who attack Ukrainian troops.
Ukraine on Tuesday launched what it called a "full-scale anti-terrorist operation" designed to flush out pro-Kremlin protesters and gunmen from state buildings across nearly 10 towns and cities in the heavily Russified east of the ex-Soviet state.
Ukraine's security service said on Wednesday it had intercepted communications showing that Russian commanders in the separatist east had issued pro-Kremlin militants with "shoot-to-kill" orders.
The intercepted communications "show that sabotage operations in the east of Ukraine are being openly led by regular officers from the Russian military intelligence, who have issued cynical shoot-to-kill orders against Ukrainian soldiers," the Ukrainian Security Service (SBU) said in a statement.