Speaking during a visit to Germany, the US President insisted the crisis is “not just a European problem”, saying: “This is our problem too.”
But he expressed concern about the “strain” it is putting the continent’s politics by “advancing far-right nationalism”.
He added: “It is encouraging a break-up of European unity that in some cases is being exploited by somebody like Mr Putin.”
Mr Obama went on to claim Putin is “not entirely persuaded” by the idea of European unity.
He told CBS: “Mr Putin has generally viewed NATO, EU, trans-Atlantic unity, as a threat to Russian power. I think he’s mistaken about that.
“I’ve indicated to him that, in fact, a strong, unified Europe working with a strong, outward-looking Russia – that’s the right recipe.”
The President also discussed his decision to send 250 additional US forces in a desperate bid to wipe out the Islamic State terror group.
He said: “It represents what I’ve said from the start, which is that us dismantling ISIS is a priority.
“And although we are not going to send ground troops in to fight, we are going to try to find out what works and then double down.”
Mr Obama’s comments came hours after a Tory minister suggested Mr Putin is less likely to “harm” the UK in the event of Brexit.
Armed Forces Minister Penny Mordaunt told Newsnight: “The trajectory [the EU] is on good news for those who wish us harm.
“We have a growing migrant crisis and all the threats that come with that. The EU is the authority without any responsibility.”
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