In her introduction to Tuesday's show, Maitlis said Cummings had "broken the rules" and "the country can see that, and it's shocked the government cannot”.
The BBC said while Maitlis had been scheduled to present the next edition of the programme, Katie Razzall would take her place. She did not address the controversy during the programme.
BBC statement on last night's Newsnight pic.twitter.com/JFm4Nt5YMv— BBC News Press Team (@BBCNewsPR) May 27, 2020
The BBC did not prevent the broadcaster from presenting Wednesday's programme, according to news agency PA.
Maitlis has since tweeted about being replaced for the night and confirmed that Razzall took her place after she asked for the night off.
She later tweeted: “Been overwhelmed by all the kindness, messages – and support on here – and I’ve probably missed much of it.”
So grateful to my friend and excellent colleague @katierazz for stepping in this evening . She did so because I asked for the night off -knowing tonight’s prog would be in the most excellent hands 🖐 #newsnight https://t.co/0ZkH2KbzBF— emily m (@maitlis) May 28, 2020
In Tuesday’s Newsnight opening, Maitlis said: "The longer ministers and the prime minister tell us he worked within [the rules], the more angry the response to this scandal is likely to be.
"He was the man, remember, who always got the public mood, who tagged the lazy label of elite on those who disagreed.
"He should understand that public mood now – one of fury, contempt and anguish.”
Been overwhelmed by all the kindness, messages - and support on here - and I’ve probably missed much of it. A big thank you from us all at #newsnight— emily m (@maitlis) May 28, 2020
Newsnight editor Esme Wren said on Twitter Maitlis had not been "replaced tonight in response to the BBC statement" and that the programme's staff "work as a team throughout”.
Razzall also said her fellow presenter had "not been asked by the BBC to take tonight off", adding that she "certainly wouldn't have agreed to present the show" if she thought that was the case.
The National Union of Journalists criticised the BBC over its handling of the row.
General secretary Michelle Stanistreet said: "At a time of national crisis, frank and fearless journalism that scrutinises and holds this government to account is more necessary than ever.”
She said it was "clear as day" that Cummings breached lockdown rules, adding: "Journalists should be congratulated for holding policymakers to account for actions that risk a monumental breach of trust during a public health crisis.”
The BBC said in a statement on Wednesday staff had been "reminded of the guidelines" around impartiality following the broadcast, adding that the corporation must "uphold the highest standards of due impartiality in its news output”.
The statement added: "We've reviewed the entirety of last night's Newsnight, including the opening section, and while we believe the programme contained fair, reasonable and rigorous journalism, we feel that we should have done more to make clear the introduction was a summary of the questions we would examine, with all the accompanying evidence, in the rest of the programme.
"As it was, we believe the introduction we broadcast did not meet our standards of due impartiality.”
So, Lord Hall said nothing as the Govt banned ministers from @BBCNewsnight for months, but humiliates @maitlis for speaking the truth about lying Cummings? This is why I’d never work for the BBC - great journalists, cowardly weasel management. pic.twitter.com/tCZ2dIIJhZ— Piers Morgan (@piersmorgan) May 27, 2020
Good Morning Britain presenter Piers Morgan branded the BBC statement "utterly disgraceful", adding that the BBC is "chucking one of its best journalists under the bus for telling the truth”.
His words were echoed by journalist and former Newsnight economics editor Paul Mason, who said the decision made him “sick".
He tweeted: "Every word Maitlis said was true: truth is the criterion of real journalism.”
Conservative MP Julian Knight, who chairs the Digital, Culture, Media and Sport Committee, said the broadcaster had responded rapidly to the incident.
The introduction to Newsnight had a clear bias and had nothing to do with the BBC's mission to inform and educate. We do not need Newsnight to behave as poor quality entertainment. https://t.co/5RILNQ8JAc— Chris Green (@CGreenUK) May 27, 2020
He tweeted: "For the BBC to come out, in such terms, so quickly is really something, no circling of the wagons – issuing what is effectively a written warning.”
The programme's introduction was criticised by Chris Green, the Conservative MP for Bolton West, who said on Twitter it "had a clear bias and had nothing to do with the BBC's mission to inform and educate”.
He added: "We do not need Newsnight to behave as poor quality entertainment.”
The Newsnight coverage centred on a trip by Cummings from London to Durham during the lockdown, with the aide saying he acted "reasonably and legally”.