Downing Street is threatening the future of the BBC by insisting it is seriously considering decriminalising non-payment of the licence fee, while boycotting Radio 4’s Today programme over the broadcaster’s supposed anti-Tory bias.

No 10 pulled ministers from Saturday’s edition of the Today programme and sources said it intended to “withdraw engagement” from the show in future.

The row is seen as an ominous sign of Boris Johnson’s willingness to bypass independent scrutiny and follows criticism of the BBC’s election coverage from both left and right.

No 10 pointed to Andrew Neil’s on-air monologue in which he lambasted Johnson for his refusal to be interviewed, and the BBC’s “extensive coverage” of a four-year-old boy with suspected pneumonia forced to sleep on a hospital floor – as supposed evidence of anti-Tory, pro-remain bias at the corporation.

Meanwhile, Labour backers have raised concerns about the BBC’s coverage, from the editing out of laughter aimed at Johnson in a news bulletin to leading reporters uncritically repeating Conservative sources, and the prime minister escaping scrutiny after dodging the one-on-one interview with Neil.

The BBC has firmly rejected such criticism. In an email on Friday, the director general, Tony Hall, wrote: “In a frenetic campaign where we’ve produced hundreds of hours of output, of course we’ve made the odd mistake and we’ve held up our hands to them. Editors are making tough calls every minute of the day. But I don’t accept the view of those critics who jump on a handful of examples to suggest we’re somehow biased one way or the other.”

During the election campaign, Johnson threatened to take the BBC’s licence fee away as he called into question its status as a publicly funded broadcaster. The prime minister suggested the licence fee, which is guaranteed to continue until at least 2027, was a general tax that could no longer be justified when other media organisations had found other ways of funding themselves.

Any changes to the BBC’s funding model would require parliament to pass fresh legislation. Abolition would be hard, but a bigger risk for the BBC is the negotiations with the government over the cost of the licence fee between 2022 and 2027.

Even more worrying for the public broadcaster are comments by chief secretary to the Treasury Rishi Sunak, confirming plans to look at the decriminalisation of failing to pay the TV licence, which could be set out in the next Queen’s speech and would undermine the BBC’s funding model.

Sunak told the BBC’s Andrew Marr Show: “That is something the prime minister has said we will look at, and has instructed people to look at that. I think it’s fair to say people find the criminalisation of non-payment of the licence fee to be something that has provoked questions in the past.”

A No 10 source confirmed that the licence fee was “in the firing line”, following reports in the Mail on Sunday that its future settlement was under discussion.

A BBC spokesperson said decriminalisation would lead to £200m less to spend on programmes.

“The government has already commissioned a QC to take an in-depth look at this matter and he found that ‘the current system of criminal deterrence and prosecution should be maintained’ and that it is fair and value for money to licence fee payers,” they said. “Decriminalisation could also mean we have at least £200m less to spend on programmes and services our audiences love.”

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Johnson’s senior adviser Dominic Cummings is known to be a strong critic of the BBC, its funding model and its output. He is particularly dismissive of the Today programme, which he argues operates in a metropolitan bubble out of touch with the rest of the country.

Downing Street has also attacked Channel 4’s election coverage after it replaced Johnson with an ice sculpture when he refused to take part in a leaders’ debate on the climate crisis.

During the election the Tories confirmed that the party would review Channel 4’s public service broadcasting obligations if Johnson was returned to Downing Street. Under the proposal it will “look at whether its remit should be better focused so it is serving the public in the best way possible”.

However, there will be voices within the Tory party who are uneasy about an all-out war with the media, particularly the BBC – both because it remains one of the most trusted institutions in the country and because of its daily influence on the news agenda.