The Queen told him: “I’ve just been talking to your Secretary of State for Health – poor man. He came for Privy Council. He’s full of…”
Mr Johnson replied: “Beans”, but the Queen continued: “He thinks that things are getting better.”
The Prime Minister replied: “They are. In the sense that we’re….”
The comment, caught on camera, came after Hancock was criticised as “hopeless” by Mr Johnson in messages revealed by the PM’s former top adviser Dominic Cummings.
Mr Cummings has said Mr Hancock should have been fired over coronavirus failings and “criminal, disgraceful behaviour” on the testing target.
The monarch and the PM, who were together at the G7 summit earlier this month, conducted their audiences by telephone since the coronavirus pandemic swept through the nation.
The Queen welcomed Mr Johnson to her private audience room, where her black handbag could be seen perched on a nearby chair.
“Good afternoon. It’s very nice to see you again,” the monarch said with a broad smile.
Mr Johnson said: “Lovely to see you again. It’s been 15 months.”
The Queen replied “Has it really? 15 months. It’s most extraordinary, isn’t it?”
They last held a face to face weekly audience on March 11 2020.
A week later on March 18 they switched to speaking on the telephone instead as the Queen prepared to socially distance herself at Windsor Castle.
She retreated to the Berkshire royal residence into what was dubbed HMS Bubble with the Duke of Edinburgh just before England went into its first national lockdown.
The meeting of the Queen, 95, with the PM in her Private Audience Room at the palace is believed to be the first time the Queen has been at the palace for six weeks since attending the State Opening of Parliament in May.
In a 1992 documentary filmed to mark her 40th year on the throne, the Queen – the nation’s longest reigning sovereign – gave her view on the importance of her meetings with her prime ministers.
“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,” she said.
“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.”
As head of state, the Queen is politically neutral and acts on the advice of her Government in political matters, but her political knowledge is immense.
Throughout her reign, she has received weekly briefings from the prime minister of the day, and dozens of government documents pass across her desk every week for formal approval.