Earlier this year, the Cabinet Office attempted to apply for an exemption from providing information and messages it considered irrelevant to the work of the inquiry, but this was dismissed by Baroness Hallett.
In response, the Government launched a legal challenge, but it was rejected by the High Court in July, which confirmed that the documents must be provided.
The inquiry is now believed to be in possession of unredacted WhatsApp messages between Johnson and 40 colleagues, including former No 10 adviser Dominic Cummings, cabinet secretary Simon Case and former chancellor Sunak.
In response to the Guardian report, Downing Street said it would not comment on “leaks” and was “concerned about selective sections of evidence” that had been “given to the media.”
“The Government set up the Covid Inquiry to establish the facts transparently and we have submitted more than 55,000 documents in support of its work,” a Government spokesperson said.
“To ensure the integrity of the investigation is not undermined, it is vital that any evidence presented is heard in its context and in its entirety, which is why we will not comment on leaks.
“We are concerned that it appears that select sections of evidence have been released to the media and all possible measures must be taken to prevent further leaks.”
In July, Johnson’s spokesman said his messages had been recovered and handed over to the investigation.
Months of Johnson messages may be missing
However, The Guardian reported that Johnson told the inquiry in his witness statement that he was unable to access the messages during the first wave of the pandemic between January 31 and June 7, 2020.