The Czech Olympic Committee announced last month it was clearing the cyclist of the doping charges that had seen him banned from the sport for months over problems with his biological passport.
But the International Cycling Union (UCI) appealed the decision Monday, as it had warned it might after president Brian Cookson said there was "a very strong indication of manipulation."
In its appeal, UCI requested that CAS set aside the Czech decision from 22 September clearing Kreuziger of any violations of the UCI anti-doping rules.
It requested that the Czech cyclist be banned from the sport for between two and four years and that all of his results since March 2011 be erased.
It also demanded that he be fined 770,000 euros ($980,000).
Following the appeal, CAS said Tuesday it had "initiated a procedure" against Kreuziger.
"The arbitration procedure is in progress and the CAS will not comment further at this time," it said.
Kreuziger's lawyer Jan Stovicek said his client had been expecting the UCI appeal.
"However, the strong arguments remain on our side," he said in a statement, insisting that the expert panel of the Cycling Anti-Doping Foundation "decided on the alleged guilt of Roman Kreuziger on the basis of incomplete and insufficient information."
Stovicek pointed out that his client suffered from a poorly functioning thyroid gland, and as the condition worsened he was required to take high doses of a substitute hormone L-Thyroxine during the time when suspicions against him arose.
"We firmly believe that common sense will prevail," he said.
The anomalies in his biological passport date from 2011 and 2012, during Kreuziger's time with the controversial Astana team, but only came to light earlier this year.
The problems with his biological passport saw the 28-year-old Tinkoff-Saxo rider, who had finished fifth in last year's Tour de France, omitted from his team's squad for this year's Tour.
He was later provisionally suspended by the UCI, forcing him to miss the Vuelta a Espana and the World Championships.