The order was in line with an earlier plan to complete the exercise early this week.
The maneuvers, which Putin ordered on Wednesday involved scrambling fighter jets to patrol Russia's western frontiers and stoked fears that the Kremlin might send troops into Russian-speaking regions in eastern Ukraine.
In Brussels, meanwhile, the ambassadors of NATO's 28 member nations will hold a second emergency meeting on Ukraine on Tuesday after Poland, which borders both Russia and Ukraine, invoked an article calling for consultations when a nation sees its “territorial integrity, political independence or security threatened,” the alliance said in a statement.
President Barack Obama has said that Russia is “on the wrong side of history” in Ukraine and its actions violate international law. Obama said the U.S. was considering economic and diplomatic options that will isolate Russia, and called on Congress to work on an aid package for Ukraine.
In return, Russia's agricultural oversight agency issued a statement Tuesday declaring the reversal of its earlier decision to lift the ban on imports of U.S. pork. It said the existing U.S. system of checks don't guarantee its safety.
Putin's economic advisor, Sergei Glazyev, said that Russia can develop financial ties with other nations to offset any potential Western sanctions.
The European Union's foreign ministers on Monday threatened Moscow with halting talks on visa liberalization and negotiations on further economic cooperation unless Russian troops on the Crimean peninsula pull back over the next three days.
The bloc's 28 heads of state and government will hold an emergency meeting on the situation in Ukraine on Thursday that will decide on imposing the sanctions if there is no de-escalation on the ground, EU foreign policy chief Catherine Ashton said.
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