Mr Keith said the Foreign Office had also redacted messages while the Department of Health had provided Matt Hancock’s messages without any redactions.
“We have very recently identified that the Cabinet Office is not alone,” he said.
“The Foreign Office has supplied to the inquiry potentially relevant WhatsApps from two special advisers, with extensive redactions.
“May we make clear we expect them to provide unredacted WhatsApp material without delay.”
Boris Johnson WhatsApps to be inspected
The inquiry has made hundreds of written requests for evidence, including from 38 government departments and quangos.
Mr Keith said that the inquiry would compare the former prime minister’s material with messages and notebooks redacted by the Government this week.
Mr Johnson has offered to assist the inquiry and Mr Keith said that the inquiry would work to compare unredacted copies with those already handed over by the Cabinet Office.
He said: “The inquiry team has been liaising with his legal team to arrange for the inspection of the unredacted WhatsApps that he had provided to the Cabinet Office, which he had returned to him.
“We expect to begin that inspection this week. The inspection will allow your team to make its own assessment as to the redactions applied by the Cabinet Office and to satisfy ourselves and ultimately you of their appropriateness or otherwise.”
The inquiry has faced criticism over its speed and size, but Mr Keith defended its pace and said it was more thorough than those in other countries which had already been completed.
“No inquiry with such wide a scope has ever proceeded with such speed,” he said.
Opening the third and final preliminary hearing earlier, Lady Hallett addressed her dispute with the Government.
“I issued a notice under Section 21 of the Inquiries Act 2005 making it clear that, in my view, it is for the inquiry chair to decide what is relevant or potentially relevant,” she said.
“The Cabinet Office disagrees, claiming they are not obliged to disclose what they consider to be unambiguously irrelevant material. They invited me to withdraw the Section 21 notice. I declined.
“They are now challenging my decision to decline to withdraw the notice in the High Court by way of judicial review. With litigation pending and as the decision-maker, I can make no further comment.”
The retired senior judge’s deadline for the Government to hand over the former prime minister’s WhatsApp messages and notebooks in an unredacted format was missed by the Cabinet Office last week, with ministers instead announcing plans to challenge the request in the courts.
John Edwards told MPs on Tuesday that ministers should not have auto-deleting messages turned on if they were using WhatsApp to conduct government business and could face prosecution if they did.
The rules say “disappearing messages” have “a role in limiting the build up of messages” but their use must not affect “recordkeeping or transparency responsibilities”, including a requirement to forward messages about government business to an official system.
Asked whether ministers should be using disappearing messages, Mr Edwards told the Public Administration and Constitutional Affairs Committee (PACAC): “I think the Cabinet Office is pretty clear that if it is government business being conducted on a non-corporate communications channel, it must be retained as part of the official record.
“So no, they shouldn’t be using disappearing messages in the conduct of government business.”
Asked what sanctions were available if ministers did use disappearing messages, Mr Edwards added: “It’s a little perilous for me to speculate on hypotheticals, but there are criminal sanctions for failing to maintain a record or destroying a record.”
Minister denies cover-up
Jeremy Quin, the Cabinet Office minister, defended the move in the House of Commons on Monday, telling MPs that the High Court case would mean lawyers and not politicians would decide “what is and what is not relevant information” for the inquiry.
Rishi Sunak, the Prime Minister, has refused to comment on the row over Mr Johnson’s messages. “It wouldn’t be appropriate for me to comment on this ongoing legal process,” Mr Sunak told The Telegraph.
Mr Johnson’s messages are likely to include discussions with key advisors such as Dominic Cummings and Cabinet ministers such as Ben Wallace and Oliver Dowden.
Mr Quin told MPs that he expected judges to hear the Government’s judicial review “very soon”, with a hearing “on or shortly after June 30”.
He denied accusations of a cover-up, saying that all Government correspondence relating to the handling of the coronavirus pandemic would be “made transparently available” to Lady Hallett’s investigation.
But he repeated the Cabinet Office’s argument that the inquiry was asking for information ministers deemed to be “unambiguously irrelevant” and that had “nothing to do with Covid” decision-making.
Some Conservative MPs criticised the Government’s position, however, arguing it should be for Lady Hallett to decide what was relevant to her investigation.
On Tuesday, Downing Street stressed it was “willing to agree another way forward” when asked whether it is committed to going ahead with legal action against the inquiry.
Mr Sunak’s official spokesman said: “You heard from the minister that we remain hopeful and willing to agree together the best way forward.
“Obviously we have explored other possibilities for resolution previously. So obviously we continue to speak to the inquiry. And as I say, we are willing to agree another way forward.”
An FCDO spokesman said: “The UK Covid-19 Inquiry has been set up to examine the UK’s response to the Covid-19 pandemic, and learn lessons for the future. The FCDO will continue to cooperate closely with the inquiry and its work.”