Michael Ask, head of Anti-Doping Denmark, on Tuesday said Riis "failed to intervene," and "it is totally unacceptable".
"As team owner and leading sports director, Riis had a greater responsibility than the others as he as the top manager had authority to make the decisions about suspending doping users and reporting them to the anti-doping authorities," Morten Molholm Hansen, head of Denmark's Sports Confederation, said.
"He has silently accepted the use of doping."
Senior Team CSC members Johnny Weltz and Alex Pedersen also were aware of the practices, Molholm Hansen added.
"Doping with cortisone was widespread and well organised in cycling until the late 1990s because it could not be detected," he told a televised news conference.
He said it was briefly replaced by blood doping.
"We are sure it is still going on. Maybe not at the same scale but it takes place," he added.
Molholm Hansen said Anti-Doping Denmark could have pressed charges against Riis, Weltz, and Pedersen, saying there was "enough to forward doping cases for anti-doping rule violations".
However, it cannot be done because the 10-year limit on doping cases meant they were out of date.
The 97-page report was based on 50 interviews with present and former riders, aides, and officials involved in cycling since 1998.
Riis revealed in 2007 that he used blood-boosting EPO to win the Tour de France in 1996. He later owned and managed CSC, which eventually became Team Tinkoff-Saxo, until resigning three months ago.
The report said Riis gave the telephone number of Spanish doctor Eufemiano Fuentes to Tyler Hamilton, telling the American rider, "Fuentes is the best in the business, with blood doping he is the doctor to go to".
Danish rider Michael Rasmussen, who was sacked by his team while leading the 2007 Tour for lying about his whereabouts when he missed pre-race doping tests, admitted in 2013 he doped for more than a decade.
The report also quoted an anonymous source saying Riis urged 2008 Tour de France winner Carlos Sastre to use doping that year, adding: "The others are using it. We know for sure that Discovery are using it."
Speaking to Cyclingnews, Sastre denied any knowledge of doping going on during his time at the CSC team.
"I was aware of what I did and what I do, but I was not aware of what others were doing," Sastre said.
"Honestly, I didn't talk about anything like that with my teammates. Never."
It also contained an allegation by Danish rider Bo Hamburger that Riis asked him in 2000 to acquire EPO, which improves aerobic capacity by artificially raising the user's red blood cell count, for German Team Telekom rider Jorg Jaksche.
Jaksche confirmed the story to investigators, but Riis rejected the allegation.
With many revelations contained in the report dating back more than eight years, a statue of limitations for doping cases applies and no disciplinary charges can be brought.
Riis and Team Tinkoff-Saxo's main sponsors, Tinkoff Bank and Saxo Bank, were not immediately available for comment.