The government department said it was bringing a judicial review challenge "with regret" - but added that there were "important issues of principle at stake".

Despite the development, it said it would "continue to co-operate fully with the inquiry before, during and after the jurisdictional issue in question".

The legal action comes after days of wrangling in which the government hesitated over handing the tranche of documents to the public inquiry over fears it would compromise ministers' and other individuals' right to privacy.

Outlining its refusal to hand over the material in its letter, the Cabinet Office again questioned whether it had "the power to compel production of documents and messages which are unambiguously irrelevant to the inquiry's work".

COVID legal challenge 'desperate attempt to withhold evidence - politics latest

Such materials include personal messages and "matters unconnected to the government's handling of COVID", it said.

It argued that requesting "irrelevant" material "represents an unwarranted intrusion into other aspects of the work of government" and that "important issues of principle are at stake here, affecting both the rights of individuals and the proper conduct of government".

It said it had explored "a number of possible avenues for resolving this difference of opinion", including offering redacted versions of the materials and "a more focused or sequential approach to the direction of the information requirements".

"We remain hopeful and willing to agree together the best way forward."

Inquiry chair Lady Hallett ordered the government to hand over the documents last week without any amendments, using a section 21 notice.

The tranche includes messages sent between former prime minister Mr Johnson and his fellow ministers and advisers during the pandemic, as well as diary entries.

But the Cabinet Office said on Thursday that Mr Johnson's messages did not cover the whole period the inquiry wants because he was using a new phone from May 2021.

A government lawyer said the former prime minister had also swapped his own legal representation recently and gave "specified legal counsel permission to access an electronic record of certain WhatsApps" over the past two days.

Then on Wednesday night, Mr Johnson "invited Cabinet Office to share this information with the inquiry".

"By working through the night, lawyers acting for Cabinet Office have now completed our review for national security and unambiguously irrelevant material and are in a separate communication providing the relevant material to the inquiry today," they added.

But the department wanted to note it had "not been able to verify the completeness of this material" given to them by Mr Johnson, saying it did not cover the "whole of the specified time period, but only the period from May 2021 when the former prime minister acquired a new phone".

It added: "We have asked Boris Johnson if he will provide to us any further messages caught by the section 21 notice."

The inquiry confirmed on Thursday afternoon that it had received a response from the Cabinet Office.

In a short statement, it said: "At 4pm today the chair of the UK COVID public inquiry was served a copy of a claim form by the Cabinet Office seeking to commence judicial review proceedings against the chair's ruling of 22 May 2023."

Further information will be provided at a preliminary hearing at 10.30am on 6 June, it said.

On Wednesday afternoon, Mr Johnson's team claimed all the information the inquiry wanted had been passed to the Cabinet Office.

His spokesman said the ex-prime minister wanted the Cabinet Office to "urgently" hand over the material, in a move that put pressure on Rishi Sunak and the government to hand over the documents.

It is understood the older messages on Mr Johnson's phone - before May 2021 - are no longer available to search because he was advised not to activate his old phone following a well-publicised security breach in April that year.

Sources close to Mr Johnson say the Cabinet Office has been aware of the old phone.

They say he has no objection to providing the content on the phone to the inquiry and has written to the Cabinet Office asking whether security and technical support can be given so the content can be retrieved without compromising security.

Responding to the judicial review, Labour's deputy leader Angela Rayner accused Mr Sunak of undermining the inquiry and said he was "hopelessly distracted with legal ploys to obstruct the COVID inquiry in a desperate attempt to withhold evidence".

Read more:
Boris Johnson hands COVID material to Cabinet Office in 'full and in unredacted form'
How Boris Johnson was 'doorstepped' in US - and the key question he failed to answer

"Instead of digging himself further into a hole by pursuing doomed legal battles to conceal the truth, Rishi Sunak must comply with the COVID inquiry's requests for evidence in full. There can be no more excuses," she said.

Daisy Cooper, the deputy leader of the Liberal Democrats, also criticised the government's decision, calling it a "kick in the teeth" for bereaved families and a "cowardly attempt to obstruct a vital public inquiry".

She said: "The government is delaying the inquiry even further and clogging up court time, all to prevent Sunak and his Conservative colleagues from having to release their messages."