Judge Iain Bonomy pointed the finger at then-Yugoslav President Slobodan Milosevic, saying: "In practice, it was Milosevic, sometimes termed the 'Supreme Commander', who exercised actual command authority over the [Serb army] during the Nato campaign."
In the late 1990s, Milosevic's forces were attempting to suppress the ethnic Albanian majority's independence campaign in Kosovo.
The region, under UN control after Nato drove out Serb forces in 1999, unilaterally declared independence from Serbia a year ago.
Mr Milutinovic and his fellow defendants at the International Criminal Tribunal for the former Yugoslavia (ICTY) - all of whom had been allies of Milosevic - had denied all the charges against them.
His five co-accused were convicted for what the judges described as a "broad campaign of violence directed against the Kosovo Albanian civilian population".
Ex-Yugoslav deputy prime minister Nikola Sainovic, ex-Yugoslav army general Nebojsa Pavkovic and former Serbian police public security service chief Sreten Lukic were found guilty on all counts and were each sentenced to 22 years in jail.
The charges included deportation and forcible transfer, murder and persecution.
Former Yugoslav army chief of staff and defence minister Dragoljub Ojdanic and ex-Yugoslav army general Vladimir Lazarevic were found guilty of deportation and forcible transfer and sentenced to 15 years.
The verdict is a confirmation that this process has been political
All five will be given credit for time already served in the tribunal's custody.
Reacting to news of the five men's convictions, Kosovo's President, Fatmir Sejdiu, told the AFP news agency he had "full trust" in the UN tribunal.
But Serbian Interior Minister Ivica Dacic, head of the Socialist Party founded by Milosevic, rejected the outcome, saying: "The verdict is a confirmation that this process has been political."
Prosecution spokeswoman Olga Kavran told the Associated Press news agency that prosecutors welcomed the judgment, saying it proved Serbian forces had engaged in a brutal campaign to drive Albanians out of Kosovo.
At the time of the conflict in Kosovo, real power lay in the hands of Mr Milutinovic's mentor, Milosevic, says the BBC's Helen Fawkes in Belgrade.
In total, the ICTY has indicted nine of the most senior Serb and Yugoslav officials for crimes alleged to have been carried out in Kosovo.
Vlajko Stojiljkovic, a senior police official close to Milosevic, was indicted but committed suicide in Belgrade in 2002. Vlastimir Djordevic, the former chief of Serbia's Public Security Department and a fugitive until his arrest in June 2007, went on trial on 27 January.
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