Mr Putin's comments appeared to open a way to resolving the East-West standoff over Ukraine.
The pro-Russian separatists behind the referendum said they had the utmost respect for Mr Putin and would consider today whether to postpone the poll.
"We call on the representatives of southeastern Ukraine, the supporters of the federalisation of the country, to postpone the referendum planned for May 11," Mr Putin said.
He said this would create conditions for dialogue between the Ukrainian authorities in Kiev and the separatists, some of whom want greater autonomy while others demand secession.
Mr Putin added that Russians troops that had been placed near the border with Ukraine during the crisis, fuelling tension with the European Union, Nato and the United States, had been withdrawn.
"We're always being told that our forces on the Ukrainian border are a concern," Mr Putin said.
"We have withdrawn them. Today they are not on the Ukrainian border."
He spoke after talks with the head of the Organisation for Security and Cooperation in Europe, who said the security and rights body would soon propose a "road map" to defuse the Ukraine crisis.