Vanessa Dougnac, who writes for several French publications including the weekly magazine Le Point and the daily newspaper La Croix, received a notice last week from the Indian home ministry saying her work was "unimical" – or hostile – to national interests.
"Her journalistic activities are malicious and critical in manner ... they create biased perception about India," the notice said.
"In addition, her activities may also provoke disorder and disturb peace."
The notice gave Dougnac, who has been based in India for 22 years and who has an Indian spouse, until 2 February to challenge the decision to cancel her permanent residency.
Reporters Without Borders (RSF) has been monitoring the situation.
"We're very concerned by this decision. This is happening as the French president is visiting ... and we want this brought up at these discussions," RSF editorial director Anne Bocandé told RFI.
The notice was issued to Dougnac a week before Macron's arrival in India, where he will be the guest of honour at the annual Republic Day military parade on Friday.
RSF said it wants all foreign journalists to be able to work in India without being intimidated, or without risking expulsion for what they cover.
Dougnac, who has reported on a number of flashpoint topics, including the ongoing Maoist Naxalite insurgency in parts of rural India, denied "all the allegations and imputations" made against her.
"India is my home, a country which I deeply love and respect, and I have never engaged in any acts that are in any manner prejudicial to Indian interests," she said in a statement.
The French press agency AFP contacted the home ministry and foreign ministry for comment.