Putin calls Obama over a US proposal for a diplomatic resolution to the crisis in Ukraine
The contact followed a call by Ukraine's ousted leader Viktor Yanukovych for a nationwide referendum which would serve Moscow's purpose of turning the country into a loosely-knit federation.
The White House said Mr Putin called Mr Obama over a US proposal for a diplomatic resolution to the crisis in Ukraine, which US secretary of state John Kerry presented to his Russian counterpart Sergey Lavrov earlier this week.
Mr Obama suggested Russia put a concrete response in writing and the presidents agreed that Mr Kerry and Mr Lavrov would meet to discuss the next steps.
"President Obama noted that the Ukrainian government continues to take a restrained and de-escalatory approach to the crisis and is moving ahead with constitutional reform and democratic elections, and urged Russia to support this process and avoid further provocations, including the build-up of forces on its border with Ukraine," the White House said.
A White House official said the presidents spoke for an hour. He said the plan was the old off-ramp road map that had been drafted before Russia annexed Crimea last week.
The Kremlin said in its account of the conversation that Mr Putin talked about action by extremists in Ukraine and suggested "possible steps by the international community to help stabilise the situation" in Ukraine. It added that Mr Putin also pointed at an "effective blockade" of Moldova's separatist region of Trans-Dniester, where Russia has troops.
Russia and the local authorities have complained of Ukraine's recent moves to limit travel across the border of the region on Ukraine's southern edge. There were fears in Ukraine that Russia could use its forces in Trans-Dniester to invade.
Yesterday's referendum statement from former president Mr Yanukovych, who fled to Russia after three months of protests, raised the threat of more unrest in Ukraine's Russian-speaking eastern provinces, where many resent the new government.
Meanwhile Russian defence minister Sergei Shoigu told Mr Putin the Ukrainian military withdrawal from Crimea was complete. Ukrainian soldiers were seen carrying duffel bags and flags as they shipped out of the Black Sea peninsula that Russia has annexed.
While Mr Yanukovych has practically no leverage in Ukraine, his statement clearly reflected the Kremlin's focus on supporting separatist sentiments in eastern Ukraine.
Deep divisions between Ukraine's Russian-speaking eastern regions, where many favour close ties with Moscow, and the Ukrainian-speaking west, where most want to integrate into Europe, continue to fuel tensions.
The Crimean Peninsula, where ethnic Russians are a majority, voted this month to secede from Ukraine before Russia formally annexed it, a move that Western countries have condemned as illegitimate. Talk percolates of similar votes in other Ukrainian regions with large Russian populations, although none has been scheduled.
Russia has pushed strongly for federalising Ukraine - giving its regions more autonomy - but Ukraine's interim authorities in Kiev have rejected such a move. The one vote that has been scheduled is a presidential election on May 25.
"Only an all-Ukrainian referendum, not the early presidential elections, could to a large extent stabilise the political situation and preserve Ukraine's sovereignty and territorial integrity," Mr Yanukovych said in a statement carried by the ITAR-Tass news agency.
He did not specify what the vote should ask or when it should be held.
Russia's state RIA-Novosti news agency quoted Alexei Mukhin, a Kremlin-connected political analyst, as saying while a nationwide referendum would be difficult to organise in each of Ukraine's provinces, the country's south-eastern regions could follow Mr Yanukovych's advice.
In Kiev, Ukrainian prosecutors opened a new investigation against Mr Yanukovych on charges of making calls to overthrow the country's constitutional order. He is already being investigated over the deaths of dozens of Ukrainian protesters who were shot dead in Kiev in February.
Mr Yanukovych's old rival, former prime minister Yulia Tymoshenko, attacked his referendum statement, accusing him of being "a tool aimed at destroying the independence of Ukraine".
Ms Tymoshenko is running in Ukraine's next presidential election, which Russia has sought to delay.
The new Ukrainian government and the West, meanwhile, have voiced concerns about a possible invasion as Russia builds up its troops near the border with Ukraine. Mr Putin has warned that Russia could use "all means" to protect people in Ukraine from radical nationalists.
While Mr Putin has said Russia does not want a division of Ukraine, he also sought to cast it as an artificial state created by the communists that includes historic Russian regions - controversial statements that raise doubts about the Kremlin's intentions.
To tamp down those fears, Russia's Foreign Ministry said Moscow allowed observation flights over the border by Ukrainian, US, German and other Western officials.
Russia also kept pushing its long-held contention that ethnic minorities in Ukraine are living in fear of the new interim authorities. The Foreign Ministry said not just ethnic Russians, but ethnic Germans, Hungarians and Czechs in Ukraine were also feeling fearful.
However, there have been no signs of such threats towards ethnic minorities in Ukraine.