Hachette's announcement came after Allen's son Ronan Farrow, who is extremely critical of his father, denounced the book group over Apropos of Nothing, originally scheduled to hit shelves next month.
"The decision to cancel Mr. Allen's book was a difficult one," a spokeswoman for Hachette said in a statement emailed to AFP, adding it would return all rights to the author.
Allegations that Allen molested his adopted daughter Dylan Farrow when she was seven years old in the early 1990s have dogged the Oscar-winning filmmaker for decades.
The 84-year-old director of Annie Hall and Manhattan was cleared of the charges, first leveled by his then-partner Mia Farrow, after two separate months-long investigations, and has consistently denied the abuse. But Dylan, now 34, maintains she was molested.
Hachette said on Monday its Grand Central Publishing subsidiary would release Allen's memoir in the United States on April 7. This sparked an immediate backlash with high-profile investigative journalist and best-selling author Ronan Farrow, brother of Dylan, saying on Tuesday he would no longer work with Hachette.
Ronan has long defended Dylan, who renewed her accusations against Allen in the wake of the #MeToo movement in early 2018.
On Thursday, dozens of employees company employees in New York staged a walkout in protest at the decision to publish the memoir. "We stand in solidarity with Ronan Farrow, Dylan Farrow, and survivors of sexual assault," the employees said in an email, Publishers Weekly reported.
The spokeswoman for Hachette said company executives had engaged in "extensive conversations" with staff and others in the past few days.
"After listening, we came to the conclusion that moving forward with publication would not be feasible for HBG," she said. She added that the imprint does "not cancel books lightly."
Allen did not immediately comment.
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