Judges at the International Criminal Tribunal for Rwanda said prosecutors had failed to prove the guilt of Andre Rwamakubaon any of the four charges he faced and ordered his release.
Rwamakuba had pleaded not guilty to charges of genocide, complicity in genocide, extermination and assassination stemming from his alleged role in the slaughter of 800,000 people, mainly minority Tutsis and moderate Hutus.
The former minister for primary and secondary education - a Hutu - was accused of ordering Tutsis in his hometown of Gikomero near Kigali and at a medical facility in the south to be hacked to death.
At the Butare University Hospital, Rwamakuba was alleged to have used an axe to kill a pregnant Tutsi woman and pulled away intravenous drips from other Tutsi patients.
"Having considered all the evidence and the arguments of the parties, the chamber finds Andre Rwamakuba unanimously not guilty on all counts in the indictment," Dennis Byron, the presiding judge, said.
Rwamakuba had argued that he was not present at the time of any of the alleged incidents and the court agreed the prosecution had not proved his involvement.
"Furthermore, the chamber heard testimony from defence witnesses, including Tutsi survivors, that the accused was not present at the time and location of the events and was not involved in the massacres that took place in Gikomero commune and at Butare University Hospital in April 1994," the judges said.
Prosecutors had been seeking the maximum sentence of life in prison for Rwamakuba.
He is only the fifth defendant to be acquitted of all charges by the Tanzania-based tribunal that has convicted 26 suspects.
Six other former government officials during the genocide are currently on trial at the tribunal for their alleged roles in the mass slaughter. Four others have already been convicted and sentenced to life in prison.