A watchdog had to prevent ministers breaching a strict code on political neutrality and independence during the search for new chairs for the BBC and the British Film Institute (BFI), the Guardian can reveal.

A Freedom of Information Act response by the Office of the Commissioner for Public Appointments (Ocpa) showed that ministers were asked to replace interview panellists for the high-profile jobs because they were “not sufficiently independent”.

The regulator has described such breaches as “threatening to undermine the independent status” of a role intended to bring “challenge and rigour” to finding appointable candidates for selection by cabinet ministers, including the prime minister.

The regulator also stepped in twice to demand changes to the panel selecting potential candidates to chair the Office for Students, which regulates universities.

It comes amid growing concern that the government is seeking to “rebalance” the boards of public bodies – particularly in the arts, heritage and broadcasting sectors – by appointing allies and blocking critics, in part to help it fight “culture wars”.

The Tory party co-chair Oliver Dowden last month caused anger when he pledged to pick a new chair for the Charity Commission who would “reset the balance” after Dowden said some charities had been “hijacked by a vocal minority seeking to burnish their woke credentials”. This year, the regulator cleared the National Trust of breaching its charitable objectives in examining links between its properties and histories of colonialism and slavery, including Winston Churchill’s house at Chartwell.

Charity bosses hit back, saying: “The commission must be above party politics.”

Ministers have also been embroiled this week in a scandal over sleaze and attempts to undermine the independent parliamentary standards watchdog.

On Thursday, Jonathan Evans, the chair of the committee on standards in public life, cited concerns about ministers “seeking to pack assessment panels with majorities of political affiliates” and called for the commissioner for public appointments to be consulted on all panellist choices. Lord Evans also called for the role to be strengthened in primary legislation so ministers could not abolish the watchdog or limit its powers if they objected to its actions.

Peter Riddell, who until last month was the commissioner for public appointments, took the action on interview panellists before the appointments were made in January and February this year. In all cases, the ministers followed his advice and appointed different panellists whom the watchdog judged sufficiently independent.

The appointments to lead the BBC and the Office for Students prompted public controversy because of their links to the Conservative party.

Richard Sharp, a former adviser to the chancellor, Rishi Sunak, who has donated more than £400,000 to the Tory party, was picked as BBC chair, while the Conservative peer and donor James Wharton was selected to oversee the Office for Students.

Also in February, Tim Richards, the founder of Vue cinemas, was selected to lead the BFI. Richards has not declared any political activity, which is defined as standing for elected office, donating to a party, or working or speaking publicly for one.

Vacancies on the boards of public bodies include a new chair for Ofwat, which regulates the water and sewage companies that have been accused of polluting seas and rivers while making substantial profits.

There are no rules preventing ministers from appointing political allies to roles leading public bodies. However, the panels selecting appointable candidates for the highest-profile positions must include a non-political senior independent panel member (SIPM).

Riddell disagreed with ministers’ choices of SIPMs, who “were not sufficiently independent as set out in the [public appointments] code”, which requires them to not be politically active, to be independent of the department and of the body concerned, and to be familiar with senior recruitment and the public appointments principles.

The individuals removed from the panels have not been named, with Ocpa citing Freedom of Information Act exemptions and suggesting this could “inhibit the free and frank provision of advice and exchange of views” and “prejudice the effective conduct of public affairs”. In a tweet last October, Riddell said he had challenged panellist choices and stressed “they need to be independent of the party”.

Riddell told the Guardian the five-strong panel assembled by the Department for Education for the Office for Students role included three people “clearly with Tory party links and arguably a fourth had some ... Also there was no one with recent higher education student experience.”

The final panel included Theresa May’s former chief of staff Nick Timothy, the former Tory MP Eric Ollerenshaw and the Tory peer Laura Wyld. There is no rule against ministers appointing politically active panel members unless they are the designated SIPM.

The Department for Digital, Culture, Media and Sport and the Department for Education, which oversaw the appointments, declined to comment.

A government spokesperson said: “The commissioner found no breaches of the code in the cases highlighted; he was properly consulted by ministers as required.” Officials stressed that the number of people declaring significant political links to the Conservatives remained low, at 2% of the the 1,500 public appointments in the last year.

Riddell said the problems with the Office for Students process made it “an outlier”, but he added: “The balance of some panels has led one to lift eyebrows … The row over that has had beneficial side-effects. The balance of panels of other big competitions have on the whole been pretty good.”

The panellists recommending the BBC chair included Catherine Baxendale, who was shortlisted to be a Tory parliamentary candidate in 2017 and gave £50,000 to the party when David Cameron was prime minister.

“The tempo has stepped up,” Riddell said of the government’s “rebalancing” of the leadership of public bodies. “Under the [Theresa] May government, May was, as you would expect, rather correct and she was concerned with getting good people to do things. She was quite robust on that. Clearly things changed two years ago and there was more of a desire to shift the balance.”

He said he had seen potential candidates with anti-Brexit views rooted out but declined to give examples, citing confidentiality. “There is a bit of a political litmus test being applied negatively as much as positively … People focus on X and Y [appointing] allies, but actually just as significant is blocking people.”

He said the practice applied particularly to national museums and galleries “where the arguments have been most intense”.

Riddell has previously warned that “some at the centre of government want not only to have the final say but to tilt the competition system in their favour to appoint their allies”. In his final report, published last month, he said ministerial restraint was “clearly under threat in more politically polarised times”. He said “this argues for reaffirming, and in some cases, strengthening the independent element in the appointments process”.