John Kelly’s apparent unease at a Nato meeting as Donald Trump suggested Germany was “totally controlled by Russia” was down to a lack of breakfast options, not the US president’s inflammatory comments, the White House has claimed.

Video of the morning meeting appeared to show the chief of staff and former US Marine Corps general squirming as Mr Trump criticised an energy deal between Germany – one of America’s closest allies – and Russia that he later said left Angela Merkel’s nation “captive” to its eastern neighbour.

In the clip, Mr Kelly quickly looks down as Mr Trump made his comment, before pursing his lips and turning away. He continues to look down and take notes while, next to him, the US ambassador to Nato Kay Bailey Hutchinson straightens in her chair and maintains a studiedly neutral expression.

Their visible discomfort continued as Mr Trump bemoaned the US’ outsized financial contributions to the alliance, many of whose members do not spend the recommended 2 per cent of their gross domestic product on defence.

But the White House suggested Mr Kelly’s reaction was caused by a poor breakfast offering, not the president’s forthright comments about a natural gas pipeline set to bring fuel from Russia to Germany.

Germany is attempting to reduce its reliance on coal and nuclear power, and plans to use gas as a stopgap while an improved renewable energy grid is implemented.

Press secretary Sarah Huckabee Sanders told The Washington Post that “[Mr Kelly] was displeased because he was expecting a full breakfast and there were only pastries and cheese”.

Ms Merkel hit back at the US president’s claim. She said: “I’ve experienced myself a part of Germany controlled by the Soviet Union and I’m very happy today that we are united in freedom as the Federal Republic of Germany and can thus say that we can determine our own policies and make our own decisions.”

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The pair met later on Wednesday on the sidelines of the summit and kept their comments polite during a press conference. Mr Trump said he had a “very, very good relationship” with his counterpart and a “tremendous relationship” with Germany. “You’ve had tremendous success and I congratulate you,” he told Ms Merkel.

The leaders did discuss the Nord Stream 2 pipeline, Mr Trump said, but he did not elaborate. The undersea conduit is opposed by the US and a number of EU member countries, who fear it could give Moscow greater leverage.

During the breakfast meeting Mr Trump said the US was helping to defend Nato countries from Russia while Germany was now planning to send “billions of dollars” to Moscow in the energy deal.