The charges relate to atrocities committed during the 1977-78 "Red Terror" period when tens of thousands of people were killed or disappeared in Mengistu's bid to turn Ethiopia into a Soviet-style workers' state.
Mengistu, who was ousted in 1991 and currently lives in exile in Zimbabwe, was known as "defendant number one" in the case against himself and other senior members, including Fikre Selassie, the ex-prime minister, of his Derg (Committee) regime.
Judge Kiros said: "The court believes that there is no justification for the Derg actions."
Another 60 co-defendants were also found guilty of genocide, but only by a majority 2-1 ruling by the judges, who acquitted some but not all on several of the lesser charges.
Only one defendant was acquitted on all charges.
Those convicted, including Mengistu, face the death penalty and their lawyers have until December 28 to file motions seeking lesser sentences, the judge said.
Robert Mugabe, the Zimbabwean president, has pledged not to deport Mengistu as long as he does not engage in political activity.
A member of Mugabe's government ruled out extraditing Mengistu to face justice.
Paul Mangwana, Zimbabwe's acting information minister, told AFP: "Comrade Mengistu asked for asylum and he was granted that asylum. That position will not change".
Mengistu is accused by his critics of killing thousands during his 17-year rule which began with the toppling of Emperor Haile Selassie in 1974 and included war, brutal purges and famine.