A government minister has said the government is likely to lose its legal case against the Covid investigation.

It comes after the government said it would seek judicial review over a request to investigate sending Boris Johnson’s unredacted messages on WhatsApp.

Science minister George Freeman, speaking at the time of the question on the BBC, said he had “little doubt” that the court would find it obligatory to turn over the documents.

He added that it was worth “testing” whether officials had a right to privacy.

On Thursday, the government missed the 16:00 GMT deadline for letters sent between Mr Johnson and 40 other ministers and officials during the pandemic to be sent out.

The Cabinet Office – which supports the prime minister in running the government – argued that many of the letters were irrelevant and that handing them over would compromise ministers’ privacy and hinder future decision-making.

Baroness Hallett, a retired judge and colleague heading the inquest, said it was up to her to decide on the relevant material.

Asked if he thought the government would win the case, Mr Freeman told the BBC he believed “the courts will probably take the view” that Ms Hallett is entitled to decide “what evidence they think is relevant”.

He added that “people’s privacy is really important” and that the question of how to handle private correspondence was “a point worth examining”.

“I would like to see a situation where the investigation says, ‘Listen, we’re going to fully respect the privacy of anything that’s not related to Covid. We’re going to redact it,’” he said.

The challenge is believed to be the first time the government has taken legal action against its public inquiry.

Johnson said he had handed his letters over to the Cabinet Office and would be “more than happy” to have them forwarded to the inquiry, unaltered.

The former prime minister did not deliver any messages before April 2021 – more than a year into the pandemic – because his phone was involved in a security breach and has not been turned on since, a spokesperson for the former prime minister said.

The spokesperson added that he had written to the Cabinet Office to ask if technical support could be provided so that content could be retrieved without compromising security.

The saga comes just weeks before the inquiry – which is tasked with outlining lessons learned from how to deal with the pandemic – holds its first public hearings.

Lobby Akinola, of the Covid-19 group Bereaved Families for Justice, expressed dismay at the government’s decision to raise the challenge and said he feared it was part of an effort to make the investigation “weak”.

“I’m frustrated, I’m angry,” he told the BBC’s The World Tonight, adding, “We’re trying to understand what went wrong so we can prevent it from happening again and that’s … what the government is holding back.”

Elkan Abrahamson, a lawyer representing the group, said the refusal to hand over the materials “raises questions about the fairness of the investigation and how open and transparent it can be if the president is unable to see all the materials.”

Opposition parties also urged the government to comply with investigation requests.

Labor deputy leader Angela Rayner described the legal challenge as a “desperate attempt to block evidence” that would only “undermine the Covid investigation”, while the Liberal Democrats called it “a kick in the teeth for bereaved families who have already waited so long for answers”.