The court found the men guilty of trying to oust the government and set up an Islamic state and sentenced them to 14-20 years in prison.
In a statement released Friday, the EU leadership questioned the veracity of the prosecution's side of the story and said the defense had been inadequate and, thus, could not have ensured a fair trial.
While acknowledging "the criminal nature" of the protesters' actions, EU leaders accused the Uzbek court of disregarding the ample evidence testifying to the disproportionateness of security forces' response.
Human rights groups say about 700 civilians died as a result of the violent crackdown of the security forces and police. The Uzbek government has said only 187 people were killed, most of them Islamic militants.
The EU again stressed the need to carry out an independent inquiry into the Andijan unrest and expressed its willingness to discuss the problem with Uzbek authorities.