"We do not seek confrontation but we will not waiver if challenged," Rasmussen said after a brief meeting with Obama in Brussels, the Belgian capital that also hosts EU and NATO headquarters.
The US president, who kicked off a daylong visit to Belgium with an emotional stop in the sole Belgian World War I cemetery to hold US graves, said later that "NATO nations never stand alone."
Recalling that the alliance now was patrolling the skies over the Baltics, and had reinforced its presence in Poland, he said: "and we're prepared to do more."
"NATO is a force for peace but also unmatched militarily," Rasmussen said.
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"Our commitment to the defence of our Allies is unbreakable and at the same time we are firm in our support of Ukraine's sovereignty and territorial integrity," the NATO chief said.
"We will intensify our military cooperation with Ukraine including helping the Ukrainians to modernise their armed forces."
Obama ruled out military action in Ukraine, which is not a member of NATO.