The report cited six women who said the longtime media executive harassed them between the '80s and '00s.
Moonves said in a statement to CBS, "I recognize that there were times decades ago when I may have made some women uncomfortable by making advances. Those were mistakes, and I regret them immensely. But I always understood and respected — and abided by the principle — that 'no' means 'no,' and I have never misused my position to harm or hinder anyone's career."
His wife, Julie Chen, said she stands behind her husband.
Moonves' alleged behavior seeped into other major branches of CBS, The New Yorker reported, citing 30 current and former employees.
"60 Minutes" Executive Producer Jeff Fager was one of the people that allowed harassment to occur, 19 current and former employees told The New Yorker. Fager is also a former chairman of CBS News.
CBS said in a statement to the New Yorker that there have been no misconduct claims or settlements against Moonves during his career at the network. It also disputed the New Yorker's characterization of its workplace culture, saying it is "mindful of all workplace issues and takes each report of misconduct very seriously."
CBS shares fell as much as 7 percent Friday on the news of the upcoming expose.
CBS stock was at one point on pace for its worst daily performance since Oct. 2, 2011, when it dropped 7.02 percent, before paring losses slightly. The stock closed 6 percent down.
Farrow won a Pulitzer Prize for his reporting on media mogul Harvey Weinstein's longstanding patterns of sexual misconduct. The revelations ultimately spurred the #MeToo movement.
Farrow addressed the report Friday afternoon, before it was published, in a tweet, saying, "If you're reading about my work from secondary sources you're often not getting the full or correct story."
The allegations against Moonves follow CBS' ouster of Charlie Rose last fall for allegations of sexual misconduct. CBS directors said in a statement to CNBC, "All allegations of personal misconduct are to be taken seriously."
Moonves has opposed efforts by Shari Redstone to merge CBS with Viacom. Redstone's National Amusements is the principal shareholder of both companies, which had split into separate publicly traded corporations in late 2005.
Viacom shares jumped 4.5 percent on news of The New Yorker's article before easing off.
In May, CBS filed a lawsuit against Shari Redstone, her father Sumner Redstone and NAI alleging that NAI's proposed CBS-Viacom merger "is not in the best interests of CBS stockholders." The Redstone family later filed a complaint alleging that CBS had no legal right to strip them of voting privileges.
A trial date was set for Oct. 3 in Delaware Chancery Court. CBS' annual meeting was set for Aug. 10 in Pasadena, California.
Here's CBS' full statement:
"All allegations of personal misconduct are to be taken seriously. The Independent Directors of CBS have committed to investigating claims that violate the Company's clear policies in that regard. Upon the conclusion of that investigation, which involves recently reported allegations that go back several decades, the Board will promptly review the findings and take appropriate action. The timing of this report comes in the midst of the Company's very public legal dispute. While that litigation process continues, the CBS management team has the full support of the independent board members. Along with that team, we will continue to focus on creating value for our shareowners."
A spokesperson for Redstone gave the following statement to CNBC Friday afternoon, in response to the CBS statement:
"The malicious insinuation that Ms. Redstone is somehow behind the allegations of inappropriate personal behavior by Mr. Moonves or today's reports is false and self-serving. Ms. Redstone hopes that the investigation of these allegations is thorough, open and transparent."