The Queen has held her first in-person weekly audience with the prime minister in 15 months, and revealed that the woes of the beleaguered health secretary Matt Hancock might not have escaped her eye.

In a short video clip of the meeting with Boris Johnson, the Queen informed him she had been speaking to “your secretary of state for health, poor man”.

Her sympathetic comment could be a reaction to the weight of responsibility resting on Hancock because of the Covid-19 pandemic, or could reflect the battering he has received from the former No 10 senior aide Dominic Cummings.

Johnson was shown in for his audience at Buckingham Palace by an equerry. “How nice to see you again,” the Queen remarked as Johnson dipped his head in bow-like fashion.

“It’s been 15 months,” he replied. “Good heavens. It’s most extraordinary,” she said. “I’ve just been talking to your secretary of state for health, poor man He came for privy council. He’s full of …”

“Beans,” added Johnson. The Queen continued: “He thinks that things are getting better.” Johnson replied: “Well, er, they are, in the sense that we’re ...” But then the video cuts off.

Hancock has been a target for Cummings, Johnson’s top former adviser, in recent weeks. In texts released by Cummings this month, the prime minister appeared to call his health minister “totally fucking hopeless” at one point in the Covid-19 crisis.

The health secretary then endured further public indignity when, as he was being driven away in a car, a journalist yelled at him: “Are you hopeless Mr Hancock?” Hancock was heard replying, “I don’t think so ...”, as the car sped off. Questioned on another occasion as the comment continued to haunt him, Hancock dismissed it as “ancient history”.

Cummings had said Hancock should have been fired over coronavirus failings, and “criminal, disgraceful behaviour” concerning the Covid-19 testing target.

It is rare to get a glimpse of what is said between the Queen and a prime minister, even rarer to hear her talking about any members of the government.

She and Johnson have not had a face-to-face weekly audience since 11 March 2020, though they were together at the G7 summit this month. The prime minister did not go to Prince Philip’s funeral in April as he gave up his place to allow in an additional relative amid the Covid-19 restrictions on numbers. Throughout the pandemic the Queen and PM have conducted their audiences by telephone.

Their meeting on Wednesday took place in the Queen’s private audience room at Buckingham Palace, London, and is believed to be the first time she has been at the building in six weeks; she attended the state opening of parliament in May. During the pandemic she has been at Windsor Castle.