Prime Minister backed Conservative Party chairman Brandon Lewis, who urged Johnson to apologise for saying Muslim women who wear a burka look like "letter boxes" and bank robbers.
Earlier, a source close to Mr Johnson reportedly said it's "ridiculous" that he's being criticised for Islamophobia.
In a message on Twitter, Mr Lewis said: "I have asked Boris Johnson to apologise".
"Clearly the Tory party has an issue with Islamophobia, but over 24 hours later the prime minister is still yet to say a word", she added.
He said he opposed a ban on the face-covering veils, but described them as "absolutely ridiculous" and compared their wearers to rebellious teenagers.
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Some suspected Mr Johnson's burka comments were meant to boost his appeal among right-wing members of the party.
Mr Johnson insisted that he had meant no harm and apologised "unreservedly" if he had offended Ms Thornberry's feelings.
Johnson's comments, in response to Denmark's introduction of a ban on burkas in public places, prompted an angry reaction from Muslim organisations and MPs, who accused him of stoking Islamophobia for political gain.
Mr Johnson is likely to be a contender to replace her.
Muslim former Tory Cabinet Minister Baroness Warsi accused Mr Johnson of copying American right wing "dog whistle" tactics to build support for a future leadership bid.
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Mohamed Sheikh, founder of the Conservative Muslim Forum, said Mr Johnson's article had been "totally out of order".
Sayeeda Warsi, a Conservative member of the House of Lords, said Johnson was using Muslim women as a "convenient political football to try and increase his poll ratings".
Meanwhile, Johnson's father, Stanley, told ITV's Good Morning Britain: "I think people are whipping up a little mountain out of a molehill on this one, I really do".
A CST spokesperson added that "it is very obvious why these comments would cause deep offence".
The resignation solidified Johnson's position as a leader of the pro-Brexit wing of the Conservative Party, which is deeply divided over its attitude to the EU.
Another Conservative MP, Nadine Dorries, said the government should apologise and that "Boris didn't go far enough".
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He immediately launched an investigation into 1MDB, which had been founded by Najib. He also said that he did not know who the owner of the luxury vessel was.
Reacting to news the first person has been fined for wearing a full-face veil in public in Denmark, Mr Johnson warned against a similar "heavy-handed" movement in the UK.