US President Barack Obama insisted on Friday Brexit would not harm transatlantic unity but warned against a bitter divorce that would undermine security in the face of a resurgent Russia.

Britain's shock vote to leave the European Union dominated Obama's final NATO summit, which comes at what he called the most critical time for the military alliance since the Cold War.

Obama used the Warsaw summit to issue a clear message to Brussels and London, but said fears that Britain's exit could cause wider destabilisation to the West were "hyperbole".

"No-one has an interest in protracted, adversarial negotiations," Obama said after meeting European Council head Donald Tusk and European Commission chief Jean-Claude Juncker.

Obama said the British vote had "created uncertainty about the future of European integration" but dismissed suggestions that this would cause the "entire edifice" of integration to crumble or damage the transatlantic relationship.

"Let me just say, as is often the case in moments of change, this kind of hyperbole is misplaced," he said.

The US president said earlier in the Financial Times that he was "confident that the UK and the EU will be able to agree on an orderly transition to a new relationship" as Britain leaves the 28-nation union.

"Given the current threats facing Europe, I fully expect that Britain will continue to be a major contributor to European security," Obama added.

NATO chief Jens Stoltenberg insisted that while Brexit would inevitably change Britain's ties to the EU, "it will not change UK's leading position in NATO."

In response to Obama's call to avoid an unpleasant break-up, Juncker toned down his previously tough position on Britain's need to start divorce proceedings immediately and accept the EU terms.

"We have to engage in negotiations. And I'm not doing this, how I could say, in a hostile mood," Juncker said.

The EU has pressed Britain to begin the negotiations immediately but British Prime Minister David Cameron -- who is to meet Obama during what will also be his final NATO summit -- stepped down last month leaving the talks to his successor, expected to be named in September.

Tusk meanwhile insisted that Brexit would not start a domino effect among the remaining 27 members of the EU, most of whom are also part of NATO.

Stoltenberg, Tusk and Juncker later signed a NATO-EU cooperation accord, laying out how the alliance can work with the EU.

The two-day NATO summit was initially meant to focus on Russia, with NATO preparing to endorse its biggest revamp since the end of the Cold War in response to Russia's 2014 intervention in Ukraine.

The summit centrepiece is a "Readiness Action Plan" to bolster NATO resources and readiness in the face of a Russia under President Vladimir Putin that the allies now see as more aggressive and dangerously unpredictable.

NATO leaders will approve rotating four battalions through Poland, Estonia, Latvia and Lithuania, up to 4,000 troops in all, as a collective tripwire against fresh Russian adventurism.

Britain said it would contribute 650 troops, with Canada, Germany and the United States will lead the other battalions.

Speaking in the home of the Soviet-era Warsaw Pact that was once NATO's chief adversary, Stoltenberg said this deployment would "make clear that an attack on one ally will be met by forces from across the whole alliance."

The plan also includes a pledge to spend two percent of annual economic output on defence, ending years of cuts, and the creation of a 5,000-strong "Spearhead" force ready to deploy within days.

Stoltenberg also sounded a conciliatory note on Russia, calling for "meaningful dialogue" as the alliance prepares to hold fresh talks with Moscow just after the summit. NATO and Russian ambassadors will meet in Brussels next Wednesday, the alliance has said.

"NATO does not want a new Cold War. The Cold War is history and should remain history," former Norwegian premier Stoltenberg said.

Moscow bitterly opposes NATO's expansion into its Soviet-era satellites, which it sees as a threat to its own security.

"We want to believe that common sense and political will to avoid a confrontation will carry the day. Russia remains open for dialogue," Kremlin spokesman Dmitri Peskov said on Friday.

Russia is even more strident in its opposition to the Ballistic Missile Defence system the United States is building and which the NATO summit is due to declare has reached an initial operating level.

Washington says the shield is designed to counter missile threats from Iran or the Middle East but Russia says that once the system becomes fully operational in 2018, it will undercut its strategic nuclear deterrent.

Separately Russia warned Friday that the US deployment of an advanced missile defence system in South Korea would have "irreparable consequences", echoing warnings by China.