The 78-year-old director has asked the New York Times, which published Dylan's letter, if he can publish a response.
"They asked and we said, 'Yes, send it in,'" Andrew Rosenthal, The Times' editorial page editor, said of Allen to the NY Times' public editor, Margaret Sullivan.
Rosenthal said they agreed to publish the response as it is a personal matter.
"Normally, we don't publish a direct response. In this case, it was so personal, we thought that we should."
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Dylan was adopted by the couple with Moses in 1987, around the same time they had their biological child Ronan.
Farrow, who broke up with Allen after coming to know about his affair with one of her adopted daughters --Soon-Yi Previn -- from an earlier marriage, filed charges of molestation against Allen during their 1992 custody battle. The case was later dropped.
Farrow and Allen's children, who remain estranged with Allen, have upped attack on Allen recently, taking pot shots at him during the Golden Globe and for his nominations at this year's Oscars for writing 'Blue Jasmine'.