Russia orders end to huge military drills near Ukraine
"I believe that the goals of snap checks have been achieved," Shoigu said during exercises in Russia-annexed Crimea on Thursday.
"The troops demonstrated their ability to ensure the reliable protection of our country," he said in remarks released by the defence ministry.
"I've made a decision to wind up the checks in the Southern and Western military districts," he said, adding that he had ordered participating troops to begin returning to their permanent bases on Friday.
The announcement came after Ukrainian President Volodymyr Zelensky on Tuesday invited Russian leader Vladimir Putin to meet with him in war-torn eastern Ukraine, saying that millions of lives were at stake following fresh fighting in the separatist conflict.
Russia's recent military drills and the buildup of troops on the Ukrainian border has led to concern in Kiev and the West of a repeat of Russia's 2014 aggression, when Moscow annexed the Crimean peninsula from Ukraine.
The EU estimated this week the number of Russian troops along the Ukrainian border at more than 100,000.
Shoigu has described the movement of Russian troops as training exercises in response to "threatening" NATO actions.
The defence ministry said that some 10,000 troops and more than 40 warships and other vessels were participating in the exercises in Crimea.
The move could affect access to Ukrainian ports in the Sea of Azov, which is connected to the Black Sea through the Kerch Strait on Crimea's eastern tip.
The European Union called it a "highly worrying development," while NATO also expressed "concern" and called on Russia to guarantee "free access" to Ukrainian ports.
Kiev has been battling pro-Russian separatists in the eastern Donetsk and Lugansk regions since 2014, with the conflict claiming more than 13,00 lives.