"I warmly greet all the victims of these hideous acts who might have felt offended by that letter which appeared in Le Monde (Tuesday). It is to them and them alone that I offer my apologies," the actress said in a letter published Sunday on the website of French daily Liberation.
Deneuve also said that there was "nothing in the letter" to Le Monde that said "anything good about harassment, otherwise I wouldn't have signed it."
France's most revered actress was among 100 prominent women to sign the open letter defending a man's right to "bother" women, complaining that the campaign against harassment had become "puritanical".
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They deplored the wave of "denunciations" which has followed claims that Hollywood producer Harvey Weinstein sexually assaulted and harassed women over decades.
They branded it a "witch-hunt" that they claim threatens sexual freedom.
"I love freedom," Deneuve wrote in the letter to Liberation. "I don't like this characteristic of our era where everyone feels they have the right... to condemn. An era where simple denunciations on social networks cause punishment, resignation, and... often media lynching," she wrote.
She also protested not being considered a feminist. She recalled that she had been among the women who had signed a manifesto "I had an abortion" in defence of abortion rights written by French feminist icon Simone de Beauvoir.
'Broken legal system'
As an actress since she was 17, Deneuve admitted that during her career she had been "a witness to indelicate situations" between men and women.
Other signatories of the Le Monde letter including author Catherine Millet and actress Catherine Robbe-Grillet welcomed Deneuve's response, saying the episode had "reaffirmed the need to preserve sexual freedom and fight media lynching".
The letter they signed "does not claim harassment is good", they said.
Canadian novelist Margaret Atwood, author of "The Handmaid's Tale", also weighed in on the debate at the weekend, labelling the #MeToo movement "a symptom of a broken legal system".
"All too frequently, women and other sexual-abuse complainants couldn't get a fair hearing through institutions - including corporate structures - so they used a new tool: the internet," she wrote in Canada's The Globe and Mail.
She said "vigilante justice" was a "response to a lack of justice - either the system is corrupt, as in prerevolutionary France, or there isn't one, as in the Wild West - so people take things into their own hands".
But she also warned: "Understandable and temporary vigilante justice can morph into a culturally solidified lynch-mob habit, in which the available mode of justice is thrown out the window."
The Le Monde letter triggered a wave of protest from feminists and victims of harassment and assault worldwide, including one of the women who has accused Weinstein of rape.
Italian actress Asia Argento, who was among the first to denounce Weinstein, said in a tweet: "Deneuve and other French women tell the world how their interiorised misogyny has lobotomised them to the point of no return."