Putin and Defense Minister Sergei Shoigu took a helicopter ride over the area after watching the exercises from a viewing tower, The Moscow Times reported.
Putin ordered the surprise maneuvers last week.
They involve up to 160,000 personnel, some 1,000 tanks and armored vehicles, 130 aircraft and 70 naval ships.
The Defense Ministry said the drill in the Eastern Military District is the largest in the country's post-Soviet history.
It is designed to test the ability of troops to perform urgent relocation over a distance of more than 1800 miles.