Although discussions between the monarch and the prime minister usually take place behind closed doors, cameras were allowed in on Wednesday to mark the resumption of their weekly face-to-face meetings.
The last time the pair spoke together in Buckingham Palace was on 11 March 2020, with weekly phone calls replacing the normal arrangement since the start of lockdown.
In her Private Audience Room on Wednesday, the Queen could be heard referring to the health secretary as “poor man”, after telling Mr Johnson that she had spoken to the minister at the Privy Council.
“He’s full of...” the Queen said, before the prime minister supplied the word “beans”. She added that it was Mr Hancock’s belief “that things are getting better” with regard to the pandemic.
The exchange comes after Mr Johnson’s former aide Dominic Cummings released messages showing the prime minister had called Mr Hancock “f****** hopeless” at the height of the pandemic.
Speaking before a joint Commons committee meeting last month, Mr Cummings attacked the health minister, suggesting he should have been fired on many occasions for coronavirus failings.
The political strategist also alleged that he displayed “criminal, disgraceful behaviour” on the Covid-19 testing target, and lied about the testing of patients discharged from hospital to care homes last year.
Mr Johnson is the 14th prime minister to benefit from the Queen’s audience since she became monarch in 1952.
In a 1992 documentary to coincide with her Ruby Jubilee, the Queen spoke about the tradition of speaking each week to the incumbent prime minister.
She said: “They unburden themselves or tell me what is going on or if they have any problems, and sometimes I can help in some way as well.
“They know I can be impartial and it is rather nice to feel one is a sponge. Occasionally one can put one’s point of view and perhaps they have not seen it from that angle.”
Former prime ministers are said to have enjoyed the experience, with David Cameron remarking that he found the meetings “very valuable”.
Additional reporting from PA