Allen's publicist, Leslee Dart, said in a statement, "Mr. Allen has read the article and found it untrue and disgraceful."
Allen has said the allegations, first made more than two decades ago, were manufactured by his ex-lover and Dylan's adoptive mother, Mia Farrow.
"It is tragic that after 20 years, a story engineered by a vengeful lover resurfaces after it was fully vetted and rejected by independent authorities," said Allen's lawyer, Elkan Abramowitz. "The one to blame for Dylan's distress is neither Dylan nor Woody."
Dylan is one of two children, including Moshe (or Moses, as he is called), whom Allen and Farrow adopted in the early '80s. The couple, who were together from 1980 to '92, also had a biological child, son Satchel (now known as Ronan Farrow).
Allegations that Allen had abused Dylan surfaced in 1992, when the couple broke up after it was discovered that Allen had been carrying on a sexual relationship with Farrow's then-19-year-old adopted daughter, Soon-Yi Previn. (Allen and Soon-Yi wed in 1997.)
A team of experts from Yale-New Haven Hospital concluded at the time that there was no abuse, Dart noted.
Police also investigated but decided not to charge Allen. Litchfield County, Conn., state attorney Frank S. Maco said at the time that he believed there was "probable cause" to charge Allen but that he decided against it to save the young girl the trauma of a trial.
Dylan told New York Times columnist Nicholas Kristof, a longtime friend of Mia Farrow's, that she, Dylan, "has been traumatized for more than two decades by what took place" and was belatedly diagnosed with post-traumatic stress disorder last year.
Kristof said that when Dylan heard Allen was to be presented with a Golden Globe lifetime achievement award last month, "She curled up in a ball on her bed, crying hysterically."