In April 2016, Huq defended suspended Labour MP Naz Shah during an interview on BBC's Today programme by comparing "alleged anti-Semitic" posts about Israel shared by Shah on social media to a photo Huq shared of Boris Johnson on a zip-wire next to Barack Obama. She also stressed the fact that Shah's comments were made before she became an MP and that some online comments should not be taken seriously.

Subsequently, Huq was accused of "trivialising racism". Huq later apologised, saying she was not "fully aware" of Shah's comments before defending her.

In September 2022, Huq was accused of making racist comments during a speech at a Labour Party fringe event running parallel to the party conference. Huq said of the Chancellor of the Exchequer Kwasi Kwarteng, who is black and a member of the Conservative Party, "Superficially he is a black man… if you hear him on the Today Programme, you wouldn't know he is black". In response, figures within the Conservative Party including its chairman demanded the whip be removed from Huq and her expulsion from the Labour Party.

Labour's Deputy Leader Angela Rayner called on Huq to apologise, describing her comments as "unacceptable". Sadiq Khan, the Labour Mayor of London and a friend of Huq, also criticised her statement, saying "What it infers is that all black people speak a certain way and all black people are working class. Rupa is not racist but that comment was".

Huq was suspended from the Labour Party for her comments on 27 September. Huq went on to tweet an apology, but the suspension still remained in place. Huq regained the whip on 3 March, in a statement she gave shortly after Huq re-iterated her apology and stated that she had undertaken and completed anti-racism and bias training.