The inquiry has received redacted messages from Henry Cook, Mr Johnson’s former assistant, who left his senior adviser role in early 2022 after working at Whitehall for nearly a decade.
However, official documents show that important information, including about the Covid rules regarding protests over Sarah Everard and England’s relations and Scotland’s pandemic responses, was initially omitted.
On Tuesday, Baroness Hallett, the chair of the inquiry, unexpectedly extended the 4pm deadline for the government to hand over Mr Johnson’s unredacted messages and notebooks by 48 hours.
The Cabinet Office had refused, but on Tuesday morning claimed it did not have the documents after all, saying they were in the hands of Mr Johnson and it was for him to submit them.
But Lady Hallett demanded testimony from a senior official, accompanied by a statement of truth confirming that the documents will not be in possession if the cabinet cannot provide them by the new deadline.
Lady Hallett has said that if the government does not cooperate she could be in breach of criminal law and fined.
A written advice to the government from Sir James Eadie KC, seen by Bloomberg, says that documents recording talks between senior ministers during Covid should not be made public “obviously” as doing so would undermine the principle of collective responsibility.
It is the convention in British politics that ministers can express dissent and expect it to remain private.
The lawyer’s advice, received last year, said the inquiry is likely to call for revelations relating to ministers still in office, and will be “extremely recent and of the greatest political sensitivity”.
It was a situation that the principle of collective responsibility must avoid, he wrote.
A source in Whitehall said the government had not redacted any material related to the collective responsibility of the cabinet.
The source added that Labor had adhered to the same rules for ensuring collective responsibility during the Chilcot Inquiry into the Iraq War.
A spokesman for the Cabinet Office added that over the past 11 months it has provided more than 55,000 documents, 24 personal witness statements, eight company statements and “a lot of time and effort” for the investigation.
The spokesperson also said that any person or witness who wishes to provide material to the Covid investigation can do so directly.
Sunak said the government acted “in a spirit of transparency and honesty”.
But a Tory source said: “The Cabinet Office pants are on fire. It has totally mishandled Boris and is now mishandling the inquiry with another day of cabinet chaos.
“There is no grip on the blob and Tory MPs are increasingly concerned.”
It emerged on Tuesday that ministers will avoid questions about the deaths of thousands of care home residents during the pandemic until after the general election, as the final public hearings of the inquiry will not take place until summer 2026.