The committee said on its website that "the values in the cyclist's biological passport did not exceed the basal (extreme) values".
It said it had "considered the expert opinions submitted by the International Cycling Union (UCI) and by the sportsman, which explain the so-called abnormalities."
However, the UCI said they may appeal the decision after president Brian Cookson had said last month that there was "a very strong indication of manipulation".
The UCI released a statement saying: "The Union Cycliste Internationale (UCI) confirms receipt of the Arbitration Committee of the Czech Olympic Committee's decision on the Roman Kreuziger case.
"The UCI takes note of the decision to acquit the rider and will consider the possibility of appealing the decision to the Court of Arbitration for Sport, as provided under the UCI Anti-Doping Rules.
"At this stage, with the relevant appeal windows opened, the UCI will not make any further comment on the case."
Dating from 2011 and 2012, during his time with the then much-tainted Astana team, the anomalies only came to light earlier this year.
The problems with the 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 on-going World Championships.
The UCI and the World Anti-Doping Agency now have a month to appeal the decision, said the Czech committee.