Theresa May has criticised her minister, Steve Baker, but said she would not sack the prominent Brexiter after he aired claims that civil servants had deliberately produced negative reports saying the economy would be damaged by Brexit to influence policy.

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May said the government would look at the evidence about the impact of Brexit on the British economy but it would not change the fact that the UK was leaving the EU.

“It’s important of course that the government looks at the analysis that is available,” she told ITV News. “But of course it’s also important that the government does what the British people want us to do. The British people want us to leave the European Union and that is what we will be doing.”

Speaking on a visit to China, the prime minister said it was right that Baker had apologised. “The ministerial code says that the minister should take the earliest opportunity to amend the record that has been given to parliament and apologise to parliament. He will do that,” she told Channel 5 News.

“He is going to apologise, he is going to ensure that the record in Hansard is correct so that parliament is not misled when that record is read in the future. That’s what the ministerial code asks him to do and that is what he will be doing.”

Raising a point of order in the House of Commons on Friday morning, Baker told MPs: “In the context of that audio, I accept I should have corrected or dismissed the premise of my honourable friend’s question.

“I have apologised to Mr Charles Grant, who is an honest and trustworthy man. As I’ve put on record many times, I have the highest regard for our hardworking civil servants. I’m grateful for this early opportunity to correct the record and I apologise to the house.”

The Brexit minister was forced to apologise after being accused of maligning the civil service for the second time in a week. He had previously told MPs that economic forecasts by officials were “always wrong”.

Play Video 1:56 Brexit minister accused for second time of maligning civil service – video

The row was sparked when Baker was asked by the Conservative MP Jacob Rees-Mogg to confirm that a Europe expert had told him Treasury officials “had deliberately developed an impact assessment model to show that all options other than staying in the customs union were bad, and that officials intended to use this to influence policy”.

As the minister stood up, his boss, the Brexit secretary, David Davis, muttered an instruction to say that it “didn’t happen” and grimaced when Baker replied that Rees-Mogg’s comment was “essentially correct” and said it would be “quite extraordinary” if true.

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Rees-Mogg was referring to an alleged conversation between Baker and Charles Grant, the director of the Centre for European Reform and an expert on EU negotiations, at a lunch at the Conservative party conference. Several individuals present at the event challenged the claim, including Grant himself and Antoinette Sandbach, a Tory MP.

After audio emerged of the exchange, Baker said his answer was based on an “honest recollection of the conversation” but he stood corrected. He added that he would apologise to Grant and clarify his comments in parliament.