The order came a day after the Kremlin confirmed it was beefing up its military presence at the border with Ukraine.
"In accordance with his (Putin's) order, from 11:00 am Moscow time (0700 GMT) the troops of the central military district ... have been put on full combat alert," Russian news agencies quoted Defence Minister Sergei Shoigu as saying.
Shoigu added that the troops were ordered on full combat alert after Putin told the military to conduct unscheduled exercises that will last between June 21 to June 28.
Russia's fresh military drills came a day after Ukrainian President Petro Poroshenko ordered a unilateral week-long ceasefire in the troubled east of Ukraine.
The Kremlin late Friday slammed Kiev's ceasefire announcement, noting it lacked an invitation to east Ukrainian rebels to begin talks.
Putin's office also demanded an apology from Kiev over the "shooting" of a border post, saying a Russian customs official had been wounded as a result of the incident.
Russia's chief of the general staff, Valery Gerasimov, said more than 65,000 troops, over 180 planes, some 60 helicopters and some 5,500 units of military equipment would be involved in the new drills.
Among key objectives of the drills will be troop movements over long d