In an address to parliament, Igor Tenyukh said he rejected criticism that he had failed to issue clear instructions to troops, but that he reserved the right to step down. Lawmakers initially refused his resignation, but later accepted it. A majority then voted to appoint Col. Gen. Mikhail Kovalyov as his replacement.
Authorities in Ukraine have come under criticism for their often-hesitant reaction to Russia's annexation of Crimea, which was formalised following a hastily organised referendum this month.
Tenyukh said he had received requests to leave Crimea from about 6,500 soldiers and family members, meaning about two-thirds of the 18,800 military personnel and relatives stationed there were so far taking their chances in the peninsula newly absorbed by Russia.
"4,300 servicemen and 2,200 family members wish to continue serving in Ukraine's armed forces and will be evacuated from the autonomous republic of Crimea," Tenyukh said.
In an apparent effort to consolidate control from Kiev, Ukrainian police forces trying to detain a prominent member of a radical nationalist movement key in recent anti-government demonstrations killed the man after he opened fire, the Interior Ministry said.