Labour has called for an inquiry into the use of WhatsApp within the government, after it emerged a health minister replaced his mobile phone before it could be searched for information relevant to £85m of deals that are subject to a legal challenge.

James Bethell, who oversaw the award of Covid contracts, is one of those under scrutiny over the way deals for personal protective equipment (PPE) and tests were allocated at the height of the pandemic.

As part of legal proceedings issued by the Good Law Project, the government is expected to disclose Lord Bethell’s correspondence including by email, WhatsApp and SMS relating to the award of £85m of contracts for antibody tests to Abingdon Health.

The secretary of state has a responsibility to preserve and search documents for information relevant to the case from the point at which judicial review proceedings were issued in late 2020, under the government’s “duty of candour”.

However, a witness statement from a government lawyer revealed Bethell replaced his phone in early 2021 and it may no longer be possible to retrieve the information about his dealings with Abingdon, although efforts are being made to recover them from his mobile phone provider.

The statement said Bethell had used his official email account as well as his private email account to send and receive emails relevant to the contracts, and that he had also used his mobile phone for SMS and WhatsApp messages. But it said Bethell had confirmed that about six months ago his phone was broken and replaced and that his new phone did not contain the phone data.

Government lawyers revealed Bethell had not been issued with a “preservation notice” requiring him to save documents because ministers’ official correspondence was routinely saved as a matter of course. However, this did not cover government business conducted by private means.

Bethell is already under investigation by the Information Commissioner’s Office (ICO) over the use of private emails for government business, prompted by revelations that his former boss Matt Hancock was using a private account at the height of the pandemic.

Labour called on the information commissioner to widen the scope of her investigation to cover discussions via instant messaging platforms such as WhatsApp.

The party’s deputy leader, Angela Rayner, said: “If ministers and their advisers really have nothing to hide then they will have no problem handing over the emails and messages showing what government business was being conducted in secret, so the public know how their money was spent and these messages are secured for the long-promised public inquiry.”

The Department of Health and Social Care (DHSC) did not respond to two requests for comment.

Downing Street admitted in July that Bethell had used private emails for government business despite denying it 24 hours earlier, but said he had abided by the guidance on copying in official accounts.

Bethell, a close ally of Hancock’s, told the House of Lords at the time: “In terms of the use of private email can I just reassure members that I have read the ministerial code, I have signed the ministerial code and I seek to uphold it in everything I do.”

He has also been criticised for failing to declare meetings with PPE suppliers that were awarded contracts and is facing a separate inquiry by the Lords standards watchdog over his sponsorship of a parliamentary pass for Gina Coladangelo, the aide Hancock had a relationship with in breach of Covid rules.

Bethell has written to the standards watchdog saying Coladangelo provided “unpaid parliamentary research support, helping me to draft speeches, engaging with stakeholders and assisting with my communications”. The DHSC blamed the failure to declare meetings on an “administrative error”.

The ICO is investigating the use of all private correspondence channels used by ministers – which could include tools such as WhatsApp – after concerns were raised about the former health secretary’s email, as well as private emails from Bethell.

The former health secretary resigned for breaching social distancing guidelines. His use of emails will form part of the investigation.

Bethell previously faced calls for his resignation after the Guardian revealed that a number of emails had been copied into his private email account. His address was copied into at least four official exchanges relating to a businessman who was attempting to get government contracts during the pandemic.

Elizabeth Denham, the information commissioner, has said the use of private channels to conduct government business was “a concerning one” and could lead people to feel there was “a loss of transparency about decisions affecting them and their loved ones”.

She said the effects of decisions taken by government especially during the past 18 months would continue for years to come. “It is through transparency and explaining these decisions that people can understand and trust them,” she added.

The ICO has said the use of private correspondence channels does not in itself break freedom of information or data protection rules. But Denham said she was concerned information in private email accounts or messaging services was forgotten, overlooked, auto-deleted or otherwise not available when a freedom of information request was later made.

“This frustrates the freedom of information process, and puts at risk the preservation of official records of decision-making. I also worry that emails containing personal detail are not properly secured in people’s personal email accounts.”