The letter, addressed to DraftKings CEO Jason Robins and FanDuel executives Christian Genetski and Matt King and dated Oct. 20, also asks the daily fantasy companies to notify the NCAA if any referees or officials have participated in fantasy sports contests.
The championship events include the NCAA men's and women's basketball tournaments, according to The New York Times, which first reported the NCAA's letter Tuesday night.
NCAA bylaws include a long-standing section "that states we will not accept advertising from sports wagering entities" during championship events, the NCAA told ESPN.Leagues and organizations often have the right to approve potential advertising partners, just as the NFL has made Super Bowl broadcasters pass on ads in the past.
Turner Sports and CBS, who both broadcast the NCAA men's tournament, declined to comment.
FanDuel does not have TV ads for college football but does advertise its NFL contests during college games.
The ban does not necessarily apply to the College Football Playoff, which is not run by the NCAA. While the CFP abides by NCAA bylaws, the organization has discretion over advertisements during its three games.
"What I can say is that we have not discussed it," CFP executive director Bill Hancock told The Associated Press. "Whether we will or not remains to be seen. We're watching the situation with great interest."
The NCAA also informed the DFS companies that the NCAA is canceling a previously agreed upon meeting regarding "the impact of your products on college sports."
"Such a meeting is inappropriate at this time in light of the fact that your enterprises appear to be under investigation by the Federal Bureau of Investigation and Congress," NCAA executive vice president Mark Lewis wrote, "and several states and their attorneys general appear to be looking into your business platform, offering and policies for their compliance with the law."
Lewis also referenced an Aug. 27 letter to DraftKings and FanDuel from NCAA president Mark Emmert, 10 FBS conference commissioners and the student leader of the Division I student-athlete advisory committee that requested the companies cease and desist offering fantasy sports games on college sporting events "because they were inconsistent with our values, by-laws, rules and interpretations regarding sports wagering, as well as possibly a violation of UIEGA [sic] and PAPSA [sic], and various state laws."
"It seems that we are not alone in our views in that regard," Lewis wrote. "We repeat that demand and ask that you please provide a written response immediately to our request that you discontinue the offering of fantasy games related to college sport."
A source within the daily fantasy industry told ESPN that neither FanDuel nor DraftKings plans to discontinue offering contests on college athletics.
FanDuel declined to comment Wednesday morning. DraftKings was not immediately available for comment.
As of Wednesday morning, dozens of daily fantasy college football tournaments were listed on DraftKings' site.
Daily fantasy operators have pointed to the Unlawful Internet Gambling Enforcement Act in terms of their legality and have insisted they are a game of skill. The UIGEA, which the NCAA supported when it was going through the legislature in 2006, includes language precluding fantasy sports that meet certain criteria from being a "bet or wager."
Then-NCAA general counsel Elsa Kircher Cole, along with Jeff Pash, executive vice president and general counsel for the NFL, and representatives of MLB, the NBA and the NHL, sent a letter to members of Congress stating the UIGEA "needs to become law in 2006 in order to preserve the integrity of our respective sports."
The NCAA views fantasy sports, both daily and traditional season-long games, as a form of sports betting.
"NCAA member schools have defined sports wagering as putting something at risk -- such as an entry fee -- with the opportunity to win something in return, which includes fantasy league games. Because of this, student-athletes, coaches, administrators and national office staff may not participate in a fantasy league game with a paid entry fee, " Mark Strothkamp, the NCAA's associate director of enforcement, told ESPN.com in a September interview.
ESPN staff writer Darren Rovell and The Associated Press contributed to this report.
NCAA bans daily fantasy from championship advertising
ESPN Chalk writer David Purdum explains the NCAA's decision to ban daily fantasy sites from advertising during championship games.