"I have no doubt that the UK will remain one of Nato's most capable members," he told the FT as alliance leaders gather for a summit.
The meeting will focus on the perceived threat from a resurgent Russia.
But it has been overshadowed by the UK's vote to leave the EU.
Obama warns on Brexit talks
Mr Obama met European Council President Donald Tusk and European Commission President Jean-Claude Juncker on Friday and told a news conference that the Brexit vote had created uncertainty over the future of European integration.
