"Whatever ultimately happens in the Operation Puerto investigation, in the case of Ivan Basso, I myself have also lost," Riis told Italian press agency Ansa.
"I find myself without the best rider in the world, but I also risked seeing the team with which I've spent so many years disappear."
Riis' Discovery Channel counterpart, Johan Bruyneel, was meanwhile was welcoming his new team leader to the American outfit.
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"We are excited about Ivan joining the team," Bruyneel said, "and we're looking forward to having him at Discovery Channel's training camp in Austin on December 3."
Riis's CSC and Basso agreed to part ways as the rider was being cleared by Italy's Cycling Federation in the Operation Puerto doping scandal.
Basso missed most of the 2006 season, including the Tour de France, because of the probe, but was cleared to race after the judge in the trial said sporting tribunals could not use evidence from the case.
"In my opinion the Spanish investigation is still a long time from finishing and I'm really afraid that nothing will come of it," Riis said.
Basso's new deal is for two seasons and reportedly worth 1.5 million euros per year.
"Ivan Basso has now been cleared by his country's top governing sports organizations which examined more than 500 pages of documents and determined on the merits that not only is there no proof of any involvement in illegal practices, but there is no justification for bringing a disciplinary proceeding against Basso," the Discovery team said on Wednesday.
Basso, who won this year's Tour of Italy and finished second to Lance Armstrong in the 2005 Tour de France during the American's final of seven Tour titles, has said he intends to contend for the Tour-Giro double next season.
"During Lance's final Tour's Ivan pushed Lance to a new level and we expect great things from him in 2007," said Discovery general manager Bill Stapleton.
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Pro Tour 2007
Basso denies taking drugs