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He also defended Ms Gray from claims attributed to allies of the Prime Minister that she has been “playing politics” ahead of its publication, expected in the coming days.
Mr Johnson is facing calls to explain why he held a secret meeting with Ms Gray after a Cabinet minister over the weekend said he did not know who had arranged it.
But on Monday, Mr Clarke said the Prime Minister attended to “receive an update” on the investigation at the behest of the civil service investigator.
“My understanding is that the meeting was instigated by Ms Gray,” the Treasury minister told Sky News.
“There are lots of practical questions here which need to be bottomed out in terms of, for example, who can be named in this report and the extent to which photographic evidence can be included. It is important that those practical dimensions are resolved.”
Mr Johnson and Ms Gray are understood to have met at least once for an update on the report’s progress while it was being drafted.
But Mr Clarke insisted the “integrity” of the Cabinet Office report should not be doubted by the meeting.
“I don’t think it would have been in any way improper – indeed, it would have been somewhat churlish to have declined to have met,” he added.
The Liberal Democrats will try to pressure the Government to publish the minutes of the meeting and detail who arranged it by issuing the demand in a “humble address” motion in Parliament as they raised fears of a “Downing Street stitch-up”.
Wendy Chamberlain, the party’s chief whip, said: “The public would be rightly angry if it turns out Boris Johnson put pressure on Sue Gray to water down her report into illegal Downing Street parties.”
Meanwhile, the Daily Mail reported an “insider” accusing Ms Gray of “playing politics” and “enjoying the limelight a little too much”.
Asked whether he would condemn that criticism, Mr Clarke told Sky: “I would.
“By repute she is one of the most fiercely independent and professional civil servants in the whole of Government and brings a vast range of experience to bear, so I don’t think there is any politics.”
Deputy Labour leader Angela Rayner called on the Prime Minister to “urgently explain” why the “secret meeting” with Ms Gray took place.
Downing Street has insisted the report should be “completely independent”, but Education Secretary Nadhim Zahawi struggled with a key question during a round of broadcast interviews on Sunday, saying he did not know who called the meeting.
The Gray report will follow the Metropolitan Police inquiry into rule-breaching events in Downing Street and Whitehall during coronavirus restrictions.
A total of 83 people were fined for events spanning eight separate days, including the Prime Minister, wife Carrie Johnson and Chancellor Rishi Sunak.
They all received one fixed penalty notice for an event for Mr Johnson’s 56th birthday in June 2020, when indoor mixing was banned.
Despite not being fined, reports suggest that Cabinet Secretary Simon Case will come in for severe criticism in the Gray report and could face heavy pressure to resign.
If I am to remain on the committee, I will resign as a PPS so that there isn't that conflict
Tory MP Laura Farris
Meanwhile, Tory MP Laura Farris suggested she may resign as a ministerial aide at the Foreign Office in order to continue in her role on the Commons Privileges Committee, which is set to investigate whether Mr Johnson intentionally misled Parliament over partygate.
Ms Farris, who is currently both a parliamentary private secretary (PPS) and a member of the committee, told BBC Radio 4’s Westminster Hour programme the two roles were “incompatible” in the circumstances, and “that has to be resolved this week”.
“One or other will go. If I am to remain on the committee, I will resign as a PPS so that there isn’t that conflict,” she said.