"Any statement to the contrary erases the identity and dignity of transgender people and goes against all advice given by professional health care associations, who have far more expertise on this subject matter than either Jo or I," he wrote in the essay published late Monday.
Radcliffe posted his views on the website of the Trevor Project, a U.S. based non-profit that supports young LGBTQ+ people, including with suicide prevention.
His comments came after the British author, who has a huge social media following, tweeted comments mocking a headline that cited "people who menstruate."
"I'm sure there used to be a word for those people. Someone help me out. Wumben? Wimpund? Woomud?" Rowling wrote.
Rowling hit back at critics, saying that "woman-hate is eternal."
Radcliffe called for more support for transgender and nonbinary people, and for society not to "invalidate their identities."
Sparkle, a U.K.-based transgender charity, told NBC News that it welcomed Radcliffe's comments.
"It's important to remember that J.K. Rowling is part of a vocal minority, overwhelmingly white, whose opinions are completely out of step," said Lee Clatworthy, acting chair of Sparkle.
On Saturday, Rowling further outlined her views in a series of tweets.
"I know and love trans people but erasing the concept of sex removes the ability of many to meaningfully discuss their lives. It isn't hate to speak the truth," Rowling wrote, adding that she had been "empathetic to trans people for decades."
Radcliffe acknowledged that Rowling was "unquestionably responsible for the course my life has taken" but said he felt compelled to speak out.
He said he hoped the author's comments wouldn't "taint" the opinions of fans of the popular books and movies, which taught that "love is the strongest force in the universe," he said.
"To all the people who now feel that their experience of the books has been tarnished or diminished, I am deeply sorry for the pain these comments have caused you," he wrote.
Rowling has yet to comment on Radcliffe's essay nor have any of his prominent co-stars, Emma Watson or Rupert Grint.
Radcliffe's comments were, however, welcomed by Human Rights Campaign, the largest U.S. LGBTQ civil rights organization, which tweeted: "Harry Potter himself affirms, 'Transgender women are women.' 1 million points to Gryffindor!"
Meanwhile, U.S. evolutionary biologist and author, Heather Heying tweeted: "Daniel Radcliffe’s statement erases the identity and dignity of women."
Author Rowling has previously come under fire for her views on LGBT+ issues.
In December, she tweeted her support of Maya Forstater, a British researcher who lost her job following a series of tweets that were criticized as transphobic.
While Rowling has also been criticized for belatedly adding a gay relationship, headmaster Albus Dumbledore, to her "Harry Potter" novels after the books were published — an action readers term "RetCon" or "retroactive continuity" that some said felt inauthentic.
Thomson Reuters Foundation contributed to this report.