While EU members' stances often differ on issues such as migration, "team spirit and looking for common interests have become very strong," Estonian Prime Minister Juri Ratas said in an interview. As well as the Brexit vote, factors including a lack of clarity over U.S. policies under new President Donald Trump are spurring cooperation, he said late Friday, Bloomberg wrote.

"With the not-so-certain future outlook regarding policies of all its global partners, the EU has become more unified," Ratas, 39, said in Valletta, Malta, as EU leaders met for the first time since Trump took office. "A clear understanding has emerged that if this union is strong, willing to cooperate and boldly takes on new initiatives, then there will be progress."

Read alsoBritain could strike 'Ukraine Plus' style Brexit deal – think-tankThe implications of last year's twin shocks from Brexit and the U.S. presidential ballot are still being felt in issues from NATO spending to elections in the Netherlands, France and Germany. EU officials used the Malta summit to say they won't let the new U.S. administration undermine their values. The new president should butt out of "European life," French President Francois Hollande said. As Trump signals a thaw with President Vladimir Putin, the bloc is close to extending sanctions against Russia over Ukraine.

Read alsoTrump Administration agrees with EU's position on sanctions against Russia – German FM"Trump or no Trump, Europe has to carry on along its path," European Commission President Jean-Claude Juncker told reporters Monday in Brussels. "Europe, in spite of recent events, should be playing its ambitious role on this continent and around the world."

For Estonia, an EU and NATO member of 1.3 million that borders Russia, defense is key, especially in light of the recent flare-up in Ukraine's long-standing conflict with Kremlin-backed separatists. The Baltic country, which broke free of communist rule as the Soviet Union collapsed and remains home to a large Russian-speaking minority, has received assurances that NATO will remain a reliable guarantor of its security, according to Ratas.

U.K. Prime Minister "Theresa May has signaled that Estonia won't be left behind and that Estonia is an important ally for NATO," said the prime minister, who's nation is due to get 800 British troops in the coming months as part of a NATO tripwire force to deter Russia. "All NATO members understand we're a trustworthy ally, be it the U.S. or Britain."

'Businesslike' Approach

Trump has sent mixed messages on NATO, calling it "obsolete," yet stressing the alliance's importance. He suggested during campaigning that the U.S. should only defend allies that have "fulfilled their obligations." While Estonia meets NATO spending goals, Baltic neighbors Latvia and Lithuania won't start doing so until next year.

Estonia sees no improvement in ties with Russia, according to Ratas. "The messages of last two-three days from Ukraine show that military actions have intensified, killing civilians," he said. "As long as part of a country's territory is occupied, we can't talk about warming relations with Russia."

With tensions in Ukraine persisting, the EU will look to maintain cooperation with NATO, according to Ratas. "The general attitude is that EU's relations with the U.S. have to be businesslike and good," he said.