On Monday, a panel of two international judges and one Albanian found Zoran Stanojevic guilty of taking part in the Racak massacre and sentenced him to 15 years in prison.
The human rights group, Amnesty International, says attempts by the United Nations mission in Kosovo to reform the province's justice system have not worked.
The accusation follows the trials of three Serbs accused of crimes committed during the 1999 conflict in Yugoslavia.
The criticisms have been echoed by UN officials who are concerned that some court decisions are being influenced by political pressure.
The UN mission in Kosovo started to rebuild the province's justice system two years ago.
From the outset, these efforts have been criticised for ethnic bias.
International judges
Officials from the Organisation for Security and Co-operation in Europe have repeatedly stated that the predominance of Albanians in the courts means members of other ethnic groups do not receive fair trials.
The UN has introduced increasing numbers of international judges and prosecutors to tackle the problem. According to Amnesty International, the policy has not worked.
On Monday, a panel of two international judges and one Albanian found Zoran Stanojevic guilty of taking part in the Racak massacre and sentenced him to 15 years in prison.
The incident, in which 45 Albanians were killed, eventually prompted Nato's intervention in the Kosovo conflict.
UN legal advisers say they believe the final verdict was based on unreliable evidence. They say the hearing was dogged by irregularities.
Trial testimony was inconsistent and forensic evidence clearly contradicted the prosecution's case.
Defence lawyers and the accused were unable to attend the reconstruction of the case having been threatened by local villagers.
Trials 'flawed'
UN officials with a close knowledge of the case said judges had considered abandoning the case, but said it was too politically sensitive to drop.
In a separate trial of two Serbs accused of war crimes last week, officials criticised the conduct of a German judge.
They say he was abusive towards court staff and witnesses, asking at one point his fellow judges, "Should we torture him?", when a witness failed to answer a question satisfactorily.
A statement released by Amnesty International on Wednesday suggests the conduct of the trials reflects the poor state of Kosovo's legal system.
It has now been a year since the UN started the introduction of international judges, but in spite of that, Kosovo's justice system continues to be seriously flawed and justice is not being conducted in a manner consistent with international human rights standards, said a spokeswoman.