The 78-year-old filmmaker says Dylan Farrow's open letter published last week by The New York Times includes "creative flourishes that seem to have magically appeared during our 21-year estrangement."
"Of course, I did not molest Dylan," writes Allen. "I loved her and hope one day she will grasp how she has been cheated out of having a loving father and exploited by a mother more interested in her own festering anger than her daughter's well-being."
Allen was investigated for the alleged molestation, but was never charged. A team of child abuse specialists from the Yale-New Haven Hospital, brought in to the case by prosecutors and police, concluded that Dylan Farrow had not been molested.
"Now it's 21 years later and Dylan has come forward with the accusations that the Yale experts investigated and found false," Allen said.
At the time of the breakup of their 12-year relationship more than two decades ago, Mia Farrow accused Allen of molesting Dylan Farrow. Allen has consistently denied the abuse allegation.
Their split followed the discovery of an affair between Allen and Mia Farrow's adopted daughter, Soon-Yi Previn, when she was 19 or 21. (Her official date of birth is uncertain.) Allen and Previn married in 1997 and have two adopted daughters.
"I still loved (Dylan) deeply, and felt guilty that by falling in love with Soon-Yi I had put her in the position of being used as a pawn for revenge," Allen said.
The "Annie Hall" and "Blue Jasmine" director again claims in his open letter that 7-year-old Dylan Farrow was coached by Mia Farrow.
"Not that I doubt Dylan hasn't come to believe she's been molested, but if from the age of 7 a vulnerable child is taught by a strong mother to hate her father because he is a monster who abused her, is it so inconceivable that after many years of this indoctrination the image of me Mia wanted to establish had taken root?" Allen said.
Dylan Farrow claimed in her letter last week that in 1992 at the family's Connecticut home, Allen led her to a "dim, closet-like attic" and "then he sexually assaulted me." Dylan Farrow didn't specify Allen's actions, but described other abusive behavior.
Allen said in his letter he believes Mia Farrow concocted those details, and they were inspired by the Dory Previn song "With My Daddy in the Attic."
"Does the letter really benefit Dylan or does it simply advance her mother's shabby agenda?" Allen said. "That is to hurt me with a smear. There is even a lame attempt to do professional damage by trying to involve movie stars, which smells a lot more like Mia than Dylan."
In his letter, Allen recounts several anecdotes to call Mia Farrow's integrity into question. He also addressed the claim by Mia Farrow that her ex-husband Frank Sinatra could be the father of son Ronan Farrow, not Allen.
"Even if he is not Frank's, the possibility she raises that he could be, indicates she was secretly intimate with him during our years," said Allen. "Not to mention all the money I paid for child support. Was I supporting Frank's son? Again, I want to call attention to the integrity and honesty of a person who conducts her life like that."
The 28-year-old Dylan Farrow, now married, currently lives in Florida under another name. Her letter caused an uproar, reawakening a case more than two decades after it made headlines. Some have challenged Dylan Farrow's account, most notably her 36-year-old brother, Moses Farrow. He told People magazine this week that "of course" Allen didn't molest Dylan Farrow, which she called "a betrayal."
Allen said his open letter "will be my final word on this entire matter and no one will be responding on my behalf to any further comments on it by any party."
He ended the letter by saying, "Enough people have been hurt."
Messages left for Dylan Farrow, Mia Farrow and Ronan Farrow were not immediately returned.