Fox settled two of them, and O'Reilly privately settled a third in 2011. The latter agreement was so secret that 21st Century Fox was unaware of it until last year, the paper said.
The payments by Fox on behalf of Ailes and O'Reilly are the focus of an ongoing investigation by the US attorney general's office in New York. Prosecutors are probing whether the company made adequate disclosures about them to investors.
Securities law requires publicly traded companies - such as 21st Century Fox and its predecessor company, News Corp. - to disclose "material" events affecting the company's finances. Both 21st Century Fox and News Corp. are controlled by Rupert Murdoch and his family.
Murdoch is a longtime friend and political ally of President Donald Trump, who fired the federal attorney in Manhattan, Preet Bharara, in March after Bharara refused to resign as part of a general ouster of US attorneys appointed by the Obama Administration.
The undisclosed complaints unearthed by the New York Times against O'Reilly were made by women who either worked for him or appeared on The O'Reilly Factor, and included allegations of verbal abuse, lewd comments and phone calls in which the women said it sounded as if O'Reilly was masturbating.
The paper identified the three women who complained about O'Reilly as Rachel Witlieb Bernstein, a producer who claimed that O'Reilly had verbally abused her in 2002 in front of colleagues; Rebecca Gomez Diamond, a Fox Business Network host, who reportedly recorded conversations with O'Reilly and settled in 2011; and former Fox anchor Laurie Dhue, who settled last year.
All three women have left Fox and are bound by confidentially agreements about their settlements, the paper said.
Fox hasn't said whether O'Reilly was ever disciplined as a result of the allegations. Ailes received US$40 million when he was forced out of the company last year. He remains a Fox consultant.
Fox News declined to comment and referred reporters to statements issued by 21 Century Fox and O'Reilly.
O'Reilly's statement, posted on his website, said: "Just like other prominent and controversial people, I'm vulnerable to lawsuits from individuals who want me to pay them to avoid negative publicity. In my more than 20 years at Fox News Channel, no one has ever filed a complaint about me with the Human Resources Department, even on the anonymous hotline.
"But most importantly, I'm a father who cares deeply for my children and who would do anything to avoid hurting them in any way. And so I have put to rest any controversies to spare my children.
He added, "Those of us in the arena are constantly at risk, as are our families and children. My primary efforts will continue to be to put forth an honest TV programme and to protect those close to me."
21st Century Fox, now headed by Murdoch's sons James and Lachlan, said, in its statement, that it "takes matters of workplace behaviour very seriously. Notwithstanding the fact that no current or former Fox News employee ever took advantage of the 21st Century Fox hotline to raise a concern about Bill O'Reilly, even anonymously, we have looked into these matters over the last few months and discussed them with Mr O'Reilly. While he denies the merits of these claims, Mr O'Reilly has resolved those he regarded as his personal responsibility. Mr O'Reilly is fully committed to supporting our efforts to improve the environment for all our employees at Fox News."
O'Reilly and Fox continue to face allegations by former Fox personality Andrea Tantaros, who claimed, in a lawsuit filed last summer, that O'Reilly and Ailes sexually harassed her.
