Andy Burnham’s intervention in the Manchester City debate has revived tensions between the Premier League and the prime minister.

Government officials are ­understood to be unhappy they were not given notice that the ­independent commission’s damning judgment of £900m of financial manipulation and “sham contracts” would be published shortly after Burnham’s address at the Labour party ­conference on Tuesday, and his response has not gone down well with several ­Premier League clubs concerned by his ­relationship with City’s owners.

In a series of interviews on Wednesday Burnham said he would be “really concerned” if City’s owners were forced to sell after being found guilty of more than 100 breaches of financial rules.

Such was the reaction that ­Downing Street felt compelled to ­clarify ­Burnham’s position on ­Thursday, with a No 10 ­spokesperson saying the prime minister had made clear that “the initial judgment is ­serious” and “there can’t be any suggestion that anyone is above the rules”.

With City appealing against the verdict, the spokesperson noted the process had to be allowed to run its course but said: “If wrongdoing is established those responsible should face the appropriate consequences.” That phrase raised eyebrows given City have been found guilty by an independent commission after a 42-day hearing that produced 7,000 pages of witness evidence, eight years after the Premier League began investigating the club.

Burnham’s apparent sympathy for City, with a warning about ­jumping to conclusions and praise for the ­owners’ investment in ­Manchester, has alarmed some clubs but the ­Premier League declined to respond.

HMRC is facing calls to get involved, with Meg Hillier, chair of the Treasury committee, asking for its response to the commission’s judgment. In a letter to John-Paul Marks, the permanent secretary of HMRC, Hillier sought assurances that the tax authority was “seized of the importance” of the case and asked whether it had requested an unredacted copy of the commission’s verdict.

The Times and Daily Mail have reported that City’s appeal will be based on evidence the club claim proves their sponsorship deals were funded by the Abu Dhabi government and not the club. The commission rejected that argument as “untrue”.

Paragraph 77 of the judgment states: “We concluded that it was an ‘explanation’ that the club had concocted well after the event in an attempt to obscure and ­conceal the realities of the Disguised ­Funding Scheme.”

Burnham has history with the ­Premier League, which he ­mentioned in Wednesday’s ­interviews by ­referencing his criticisms of its ­prosecution of his club, Everton, for financial rule breaches after they were docked 10 points – reduced to six on appeal – by an independent commission three years ago.

Andy Burnham with the Manchester City chair, Khaldoon Al Mubarak, at Vincent Kompany’s testimonial in 2019. Photograph: PA Images/Alamy Live News

In November 2023, Burnham, when mayor of Greater Manchester, wrote to the Premier League chair, Alison Brittain, accusing the league of an “abuse of process” and claimed Everton were being used as a pawn in efforts to show an independent ­regulator was not required in football.

Burnham made similar ­complaints on Wednesday despite ­Everton ­having admitted ­breaching ­profitability and sustainability rules, with the club contesting only the extent of the breach and sanction. “I remember people proclaiming Everton guilty at the time and, with hindsight, I think more people would say that wasn’t fair the way that was handled,” he said. “I still hold the view very firmly that they weren’t fairly treated in that process.”

The Premier League was unhappy with Burnham’s behaviour in 2023, particularly as his office posted on X two letters of complaint he sent to the league, but did not publicise replies sent by Brittain that explained the competition’s financial regulations governance process.

The Independent Football Regulator chief executive, David Kogan, has made clear he will not tolerate political interference in his role, telling the Times last year that he would resign if he sensed ­government pressure.

The City case has the potential to present an early test of his ­mettle and the IFR’s powers, given ­Burnham’s previous working relationship with the club’s owner, the Abu Dhabi United Group (ADUG), and the £25bn annual UK-Abu Dhabi ­trading ­relationship. One of Burnham’s first calls after he succeeded Sir Keir Starmer in July was with Sheikh Mohamed bin Zayed Al Nahyan, ­president of the United Arab ­Emirates and the ultimate owner of ADUG.

Kogan confirmed the IFR was monitoring the case and has powers “to assess the suitability of owners, directors and executives” to protect “honesty and integrity of English football where there is clear evidence of wrongdoing by individuals”.

City’s owners are unlikely to fall foul of the licensing system that will be introduced next season, because that is an assessment of financial sustainability and separate from the new owners, directors and senior executives test, which the IFR uses to examine honesty and integrity.

The Premier League and IFR declined to comment.