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 this week, and Burnham’s response has not gone down well with several Premier League clubs concerned by his relationship with City’s owners.

The Premier League published a redacted 40-page version of the commission’s report on Tuesday within hours of Burnham’s first keynote speech as leader at the Labour party conference.

Burnham responded in a series of interviews on Wednesday by saying 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, although he did add that he could not “intervene more in the process”, which remains subject to appeal.

City’s disciplinary fate lies in the hands of an independent commission and pending its final judgment the owners’ suitability to remain running the club could be assessed by the Independent Football Regulator (IFR), with no role for the Premier League or government.

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

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 brought up his previous criticisms of the Premier League over 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.

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,” Burnham 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.

His apparent expression of sympathy for City, with a warning about jumping to conclusions and praise for the owners’ investment in Manchester, has also raised eyebrows at the Premier League, although it does not intend to respond.

The IFR 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.