Some of the former PM’s chats from before May 2021 are still not with the group – despite the government losing a legal battle forcing him to give them up.
Westminster had until 4pm on Monday to hand over the relevant material to the inquiry after the Cabinet Office court loss.
But it has been reported that neither the government nor Mr Johnson’s team can access messages on the phone.
The phone, which Mr Johnson used until May 2021, is with the ex-PM’s lawyers.
It has prompted Whitehall officials to formally notify the inquiry why they have not yet been able to send them the correspondence.
Inquiry chair Baroness Hallett had requested access to WhatsApp messages on Mr Johnson’s devices from a group chat set up to discuss the pandemic response.
She also asked to see WhatsApp messages he exchanged with a host of politicians, including then-Chancellor Rishi Sunak, as well as various civil servants, including the UK’s top civil servant Simon Case.
But the mobile phone has been turned off and securely locked away since May 2021, due to a security breach.
Mr Johnson was forced to change his mobile phone in 2021 after it emerged his number had been publicly available online for 15 years.
The rest of the messages the High Court ruled should be shared with the inquiry were sent on Monday morning.
BBC political editor Chris Mason says there is widespread irritation within government at the failure to comply with the inquiry’s demand to be sent Mr Johnson’s messages.
Access to a mobile phone conventionally requires knowledge of a passcode – which only the phone’s owner would normally know.
Mr Johnson’s phone – which he used during crucial periods of the Covid pandemic – is currently with his lawyers.
Government officials have attempted to help Mr Johnson access the data on the phone, while in the company of his representatives, it has been claimed.
But the phone has never been in the sole possession of the government, as it belongs to Mr Johnson.
Mr Johnson’s team say ‘he will be happy to disclose any relevant material to the inquiry when it is accessible’ and insist ‘full cooperation is underway’.
The government had attempted to block an order by inquiry chair Baroness Hallett to have access to Mr Johnson’s WhatsApps, diaries and notebooks in full.
In an unprecedented step, the government launched a judicial review of the order. But the High Court rejected the government’s argument, ruling inquiries should be allowed to ‘fish’ for documents.
Mr Johnson said he was ‘more than happy’ for the inquiry to see his unredacted messages. The former prime minister previously said he had handed over WhatsApp messages, diaries and personal notebooks to the Cabinet Office in unredacted form.
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