Zineb El Rhazoui, who has joint French and Moroccan nationality, has been summoned for an interview that is the first formal step in a procedure that could lead to her being fired, she revealed to Le Monde newspaper this week.
A spokesperson for the paper on Friday insisted that the meeting's only purpose was to "remind her of her minimum obligations to her employer, following a number of incidents", without explaining what those incidents were.
El Rhazoui and her husband received death threats in February, as she was appearing on TV programmes and at conferences in France, Canada and the US to defend secularism and the right to commit blasphemy in the light of the attacks.
El Rhazoui, a sociologist who became known for her opposition to the Moroccan government and the obligation to observe the Ramadan fast in Muslim-majority countries, was recruited by Charlie Hebdo during the 2011 Arab Spring.
She declared herself "shocked" by the summons, pointing out that her husband has lost his job and had to leave Morocco due to threats from fundamentalists and that she is in virtual hiding.
"You can't criticise people for not being well and not being good workers, we're living in chaotic conditions," she told Le Monde. "It's impossible to do reporting when your under police protection."
Rhazoui believes that she is being punished for being one of 15 of Charlie Hebdo's 20 employees who publicly called for an equal share in the paper's ownership.
It is now owned 40 per cent by the family of the former editor Charb, who was killed in the January attack, cartoonist and 40 per cent by new editor Riss, who was wounded, and 20 per cent by financial director Eric Portheault.
An email was sent to the critics, calling on them not to make their disagreements public.
The paper has received nearly 30 million euros in donations and sales income since the January attack.