The Queen was filmed chatting during a garden party at Buckingham Palace on Tuesday about the delegation's "extraordinary" behaviour during a state visit by President Xi Jinping in October.
Foreign Secretary Philip Hammond confirmed that the Chinese state visit "got a bit stressful on both sides".
But, on Wednesday, the Chinese Embassy in London denied the visit had been problematic. A statement said: "President Xi Jinping's state visit to the UK last year was very successful. Both sides at the working level made great efforts towards the success of the visit."
She made the comments about the highly sensitive Chinese state visit on the same day that Prime Minister David Cameron was also filmed telling her that Nigeria and Afghanistan were "fantastically corrupt countries."
The Queen was introduced to Commander Lucy D'Orsi, who was commander of the policing operation for the Chinese state visit last October, during the monarch's first garden party of the season at Buckingham Palace.
She commiserated with Commander Lucy D'Orsi that it was "bad luck" to be the senior commander during the state visit.
She was overheard telling Commander D'Orsi that the Chinese delegation was "very rude" to the British ambassador to China, Barbara Woodward.
Commander D'Orsi agreed and said that the Chinese delegation walked out on her and Ambassador Woodward which she described as "very rude and undiplomatic".
Chinese President Xi Jinping and his wife Peng Liyuan visited the United Kingdom in October 2015.
At the time the Queen described the first state visit by a Chinese premier for 10 years as "a milestone in the unprecedented year of co-operation and friendship between the United Kingdom and China."
The state visit has so far been perceived as highly successful both in China and in the UK.
Speaking on a visit to Gibraltar, Mr Hammond said: "We had a major state visit last year, it was hugely successful.
"Big state visits are big logistic challenges.
"I was involved in this and yes, at times it got a bit stressful on both sides.
"But it was a great state visit - everybody agrees, hugely successful - and our relationship with China is very strong and has been greatly strengthened by the success of that visit."
David Cameron was praised for taking a different path from China's rivals, a strategy that according to the Global Times would help Beijing improve ties with the West.
The Prime Minister, however, has been less than praised for being caught on camera telling the Queen about an anti-corruption summit he is hosting in London on Thursday which will see "leaders of some fantastically corrupt countries coming to Britain."
The PM then went on: "Nigeria and Afghanistan - possibly two of the most corrupt countries in the world."
Mr Cameron's comments threatened to become a diplomatic incident, when Nigerian president Muhammadu Buhari said his government was deeply "shocked and embarrassed" by the comments.
Meanwhile, Prince Charles ignored questions about whether he shares his mother's view that the Chinese were rude during the recent state visit as he arrived at Fortnum and Mason.