Putin, speaking after a meeting with Swiss President Didier Burkhalter in Moscow, said he had asked for the postponement of the referendum, planned for Sunday in the eastern Ukrainian regions of Donetsk and Luhansk, to create "proper conditions" for dialogue.
"We're always being told that our forces on the Ukrainian border are a concern," Putin told reporters. "We have withdrawn them. Today they are not on the Ukrainian border, they are in places where they conduct their regular tasks on training grounds."
Putin, who has vowed to protect ethnic Russians in the former Soviet republic, also called for an immediate halt to all "military and punitive operations" in the region, where separatists have seized government buildings in at least a dozen cities and towns.
"This method of settling the internal political conflict is not a reliable way of resolving all political disputes," Putin was quoted as saying by Russia's Itar-Tass news agency. "On the contrary, they deepen the divisions."
Ukraine's transitional government launched an offensive late last week to reclaim regions under the control of the separatists, who Ukrainian and Western leaders contend were armed and instigated by Moscow after the ouster of its ally, President Viktor Yanukovich, in February.
In March, Russia annexed the Crimean peninsula after a referendum on secession from Ukraine, and supporters of Ukrainian unity fear that Russia is trying to repeat the tactic.
Despite Putin's conciliatory comments Wednesday, there was no immediate sign that the Kremlin's allies were backing down. A protest leader in Donetsk, Alexander Vaskovsky, told Russia's RIA Novosti news agency that there was no need to put off a referendum.
"I'm extremely negative about this," he was quoted as saying.
There was also no evidence of a change in Russia's military posture along Ukraine's eastern border, the White House said Wednesday. An estimated 40,000 Russian troops have been massed along the frontier, holding what Russian officials say are military exercises.