Moses Farrow, 36, told People Magazine, he believed their mother had used the accusations to turn the children against Woody Allen.
Dylan Farrow recently renewed the abuse claim after speaking out in an open letter last week.
The authorities investigated her allegation at the time, but Woody Allen was not charged.
The film director has called the allegations “untrue and disgraceful” through his publicist.
Moses Farrow told the magazine his mother had “drummed it into me to hate my father for tearing apart the family and sexually molesting my sister”.
“I see now that this was a vengeful way to pay him back for falling in love with Soon-Yi.”
Mia Farrow and Woody Allen split in 1992 after she discovered he was having an affair with Soon-Yi Previn, Mia Farrow’s adopted daughter with a former partner.
Woody Allen wed Soon-Yi Previn in 1997, and the two remain married.
Dylan Farrow told People Magazine her brother’s comments were “such a betrayal to me and my whole family”.
“My memories are the truth and they are mine and I will live with that for the rest of my life,” she said, denying her mother had coached her to accuse Woody Allen.
Dylan Farrow has previously said she decided to break her silence after two decades, when Woody Allen’s latest film, Blue Jasmine, was nominated for an Oscar.
Mia Farrow has not directly responded to Moses’ statements but tweeted: “I love my daughter. I will always protect her. A lot of ugliness is going to be aimed at me. But this is not about me, it’s about her truth.”
The New York Times, which originally published Dylan Farrow’s open letter, said on Wednesday it may publish a response from Woody Allen.
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