The letter was signed by 100 French women and said the flurry of accusations against powerful men since the Harvey Weinstein scandal has gone too far.
In France and beyond the letter, published in Le Monde, was widely condemned.
Deneuve, 74, best known for playing a bored housewife who spends her afternoons as a prostitute in 1967 film Belle du Jour, has written a new letter apologising to abuse victims.
However, she has also defended her view men are becoming victims of a “media lynching” which threatens sexual freedom.
She said “obviously nothing” in the original letter “claims that harassment is good”.
Writing in French paper Liberation, founded by philosopher Jean-Paul Sartre, she said: “I greet, sincerely, all the victims of odious acts that may have felt aggrieved by the letter published in Le Monde.
“It is to them and to them alone that I apologise.”
She acknowledged signing the original letter but said she disagreed with the way some of those who signed it “claim the right to spread” a “distorted spirit” of the text.
The original letter said that campaigns like #MeToo and its French equivalent #Balancetonporc (Call out your pig) that have stemmed from the Weinstein scandal have gone too far and threaten hard-won sexual freedoms.
“Legitimate protests against the sexual violence that women are subject to, particularly in their professional lives”, had turned into a “witch-hunt”, it claimed.
“Rape is a crime, but trying to seduce someone, even persistently or clumsily, is not – nor is men being gentlemanly a macho attack,” the letter said.
“Men have been punished summarily, forced out of their jobs when all they did was touch someone’s knee or try to steal a kiss.”
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Men had been dragged through the mud, they insisted, for “talking about intimate subjects during professional dinners or for sending sexually-charged messages to women who did not return their attentions”.
Ms Deneuve defended her feminist credentials in her rebuttal letter, saying she publicly backed legalising abortion in France.