EU External Relations Commissioner Benita Ferrero-Waldner, who recently visited Tripoli to press for the release of the condemned nurses and doctor, reiterated a call for a rethink of the case in a Supreme Court ruling.
The court decision on Tuesday "is a matter for serious concern", she said, underlining the EU's doubts about how the case had been dealt with.
"We have been extremely disappointed by the procedures in this trial," she added, noting in particular that human rights lawyers had been denied visas to represent their clients.
On Tuesday a Libyan court acquitted 10 police officers accused of having used torture to extract confessions from the five Bulgarian nurses and a Palestinian doctor.
The six medical workers were condemned in May 2004 after being convicted of deliberately infecting more than 380 children, 47 of whom later died.
"We have been extremely disappointed by the procedures in this trial"
Benita Ferrero-Waldner, EU External Relations Commissioner
Ferrero-Waldner noted that she had been "encouraged" during a 24-25 May visit to Tripoli by assurances that international legal standards would be respected, both in the police torture case and the case against the medics.
"In the light of [Tuesday's] decision I feel impelled to reiterate that it is essential that all elements of both cases be fully taken into account in order to dispel any doubt about the due process of law," she said.