The massive military exercise in western Russia involving 150,000 troops, hundreds of tanks and dozens of aircraft was supposed to wrap up anyway, so it was not clear if Putin's move was an attempt to heed the West's call to de-escalate the crisis that has put Ukraine's future on the line.
It came as Kerry was on his way to Kiev to meet with the new Ukrainian leadership that deposed a pro-Russian president, and has accused Moscow of a military invasion in Crimea. The Kremlin, which does not recognize the new Ukrainian leadership, insists it made the move in order to protect Russians living there.
On Tuesday, Russian troops who had taken control of the Belbek air base in the Crimea region fired warning shots into the air as around 300 Ukrainian soldiers, who previously manned the airfield, demanded their jobs back.
About a dozen Russian soldiers at the base warned the Ukrainians, who were marching unarmed, not to approach. They fired several warning shots into the air and said they would shoot the Ukrainians if they continued to march toward them.
The shots reflected tensions running high in the Black Sea peninsula since Russian troops - estimated by Ukrainian authorities to be 16,000 strong -tightened their grip on the Crimea Peninsula over the weekend.
Ukraine has accused Russia of violating a bilateral agreement on conditions of Russian lease of a naval base in Crimea that restricts troops movements, but Russia has argued that it was acting within the limits set by the deal.
There was no fighting elsewhere in Crimea early on Tuesday. A supposed Russian ultimatum for two Ukrainian warships to surrender or be seized passed without action from either side, as the two ships remained anchored in the Crimean port of Sevastopol. Russian Defense Ministry spokesman Vladimir Anikin said late Monday that no ultimatum had been issued.
Early on Tuesday, the Kremlin said Putin ordered troops participating in military exercises alongside Russia's western border to return to their permanent bases. The order was in line with an earlier plan to complete the exercise early this week. The massive war games have stoked fears that the Kremlin might use the troops to seize territory in pro-Russian areas of 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.
And Putin's economic advisor, Sergei Glazyev, said that Russia can develop financial ties with other nations to offset any potential Western sanctions.