"Your order to withdraw the contingent of Russian forces from Syria has been carried out," Shoigu said during a meeting of top Russian military brass in Moscow.
He said a total of 36 planes and four helicopters have returned to their permanent bases, while 157 motor vehicles were delivered to Russia by sea.
Special forces troops, a medical unit, a battalion of military police, doctors and deminers have been brought back to Russia, he added.
Russia became involved in the multi-front conflict in September 2015, when it began an aerial campaign in support of President Bashar al-Assad's military. It acknowledged in recent months that its special forces are also active on the ground in the offensive against Islamic State jihadists.
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Three battalions of military police and officers of the Russian Centre for Reconciliation will remain in Syria, Shoigu added, as well as its two bases in the country.
This week Russia's lower house of parliament ratified an agreement with Damascus to expand the naval facility in Tartus. The Senate is expected to ratify the deal next week.
Shoigu also said that Russian military ships and submarines armed with "high-precision weapons" will remain permanently present in the Mediterranean.