"At this point, all commanding structures and troops have returned to their permanent bases," Shoigu said at a meeting with President Vladimir Putin.
The Russian leader said the results of the snap drills have generally been assessed as positive.
Some 80,000 troops, thousands of ground vehicles, as well as dozens of ships, submarines, aircraft and helicopters have taken part in the drills.
Unannounced checks of combat readiness of all branches of the Russian Armed Forces have become regular since Shoigu assumed his post in November 2012. According to the Defense Ministry, in 2015 Russia will hold at least 4,000 military drills.