The article, which had already prompted over 300 complaints to the press watchdog by the end of business on Monday, said that it was not appropriate for a “young lady wearing a hijab” to cover the killings which left more than 80 dead.
The Channel 4 News spokeswoman called it “completely unacceptable, and arguably tantamount to inciting religious and even racial hatred”.
She said: “It is wrong to suggest that a qualified journalist should be barred from reporting on a particular story or present on a specific day because of their faith. Fatima Manji is an award-winning journalist.
“We are proud that she is part of our team and will receive, as ever, our full support in the wake of his comments.”
MacKenzie’s claim that Fatima Manji’s presence in the French city was “massively provocative” and a sign of “editorial stupidity” was slammed as “gutter journalism” by Tory peer Baroness Warsi and widely condemned online.
A source told the Guardian that the tweet was removed “because [it] did not make clear that the piece was by MacKenzie, and not by the Sun.”
The Huffington Post UK could not find any examples of where the column had been tweeted again by The Sun. Reader comments on the article also appeared to be turned off.
When approached by HuffPost UK a spokesperson for The Sun simply said: “No comment.”
MacKenzie wrote: “After Jon Snow had conducted a poor interview with a young man who had come perilously close to death the action switched back to the London studio, where I could hardly believe my eyes.
“The presenter was not one of the regulars — Krishnan Guru-Murthy, Matt Frei or Cathy Newman — but a young lady wearing a hijab.
“Her name is Fatima Manji and she has been with the station for four years. Was it appropriate for her to be on camera when there had been yet another shocking slaughter by a Muslim.
“Was it done to stick one in the eye of the ordinary viewer who looks at the hijab as a sign of the slavery of Muslim women by a male- dominated and clearly violent religion?”
The column provoked a massive reaction on Monday morning with many fellow reporters coming to the defence of Manji while Baroness Warsi wrote an open letter to editor in chief, Tony Gallagher.
On Friday night after the programme, Manji tweeted that her presenting was “long planned”. “Had thought it might be a quiet Friday, instead very tragic,” she tweeted.
MacKenzie continued: “With all the major terrorist outrages in the world currently being carried out by Muslims, I think the rest of us are reasonably entitled to have concerns about what is beating in their religious hearts. Who was in the studio representing our fears?”
Channel 4 said they would respond to the column in due course.
Hate crime hotline Tell Mama told HuffPost UK: “Mackenzie seems to believe that all Muslims are somehow at fault for the actions of terrorists and extremists. He uses the term ‘Muslim’ terror attack when the picture of the perpetrator is of a broken man who had numerous issues and who was hardly Muslim in his actions.
“Instead of writing an article about tackling extremism and terrorism together as communities, he turns on Fatima Manji and inadvertently suggests that any Muslim who comments or is in the public eye should be removed, by default because of the association of their faith to that of the perpetrator even though it seems he was hardly Muslim in his lifestyle.
“What we have in the comments of MacKenzie is someone who believes in ‘collective punishment’. Remove those who are Muslim because someone who was born of a Muslim mother conducts a crime. This is stomach-churningly autocratic, perverse and very dangerous.”
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