Wanted for his role in the 1994 Genocide against Tutsi, Mpiranya was a presidential guard commander during the Genocide.
UN prosecutors recently announced that he died in Zimbabwe where he fled years earlier, following pulmonary tuberculosis.
He was buried in a cemetery near Harare under an alias, with his family and associates carefully hiding his death.
In a statement released on Sunday, Zimbabwe has refuted media reports that it sheltered the Genocide fugitive.
"The Government of Zimbabwe wishes to clarify some recent media reports that are circulating insinuating that the Government was harbouring the most wanted Rwandese fugitive, Protais Mpiranya," reads part of the statement.
"Contrary to a smear campaign peddled by both international mainstream media and social media seeking to portray Zimbabwe as aiding, abetting and hiding a fugitive, the government of Zimbabwe actually assisted the UN Prosecutor in the identification of Mpiranya."
Mpiranya was indicted in 2000 by the International Criminal Tribunal for Rwanda (ICTR) on eight counts of genocide including complicity in genocide, murder, extermination, rape, persecution, other inhuman acts constituting crimes against humanity, and murder.
He was accused of killing Prime Minister Agathe Uwilingiyimana, 10 Belgian peacekeepers charged with protecting her and several prominent politicians, as well as their families and servants.
It is said that Mpiranya fled to Cameroon following the 1994 Genocide against the Tutsi.
In 1998, he returned to Zaire and joined the second Congo war siding with President Laurent-Désiré Kabila with intentions to fight Rwanda.
While in the country, Mpiranya worked with Zimbabwean troops supporting Kabila and later sought refuge in Zimbabwe where he found shelter towards the end of 2022.
Sources reveal that Zimbabwean leaders facilitated him to enter the country along with close allies.
Mpiranya run businesses including transport company carrying goods and people using two vehicles bought from minerals stolen in Congo.
His business did not succeed and according to acquaintances, he health started deteriorating due to poverty.
Mpiranya lived in a standalone villa the first year upon arrival in Zimbabwe but was later hit hard that he was obliged to share a villa with other tenants.
Investigators revealed that Mpiranya used to meet with top leaders on the rehime of President Robert Mugabe who led the country from 1987 to 2017. Mugabe died in 2019.
IRMCT revealed that Mpiranya fell critically ill suffering from pulmonary tuberculosis in 2006 where he was admitted at West End Hospital in Harare.
He died on 5th October 2006 and buried outside Harare under false names of Ndume Sambao.
IRMCT report released between 1st July 2020 and 30th August 2021 indicated that the collaboration with Zimbabwe progressed well unlike the situation at the leadership of Mugabe.
The report revealed that the country’s Prosecution increased collaboration with Zimbabwe and commended the country’s support.
The statement by Zimbabwe indicates that officials had cooperated with investigators seeking Mpiranya, setting up a joint working group, helping to finance the research, sharing investigative reports as well as summaries of interviews with suspects.
"It was the Government of Zimbabwe that authorised and participated in the exhumation of Mpiranya’s remains when it was suspected that he was the one buried under a false name, Ndume Sambao," the statement added.
The government further said that Zimbabwe would never harbour criminals and welcomes the result of DNA samples taken from the fugitive which "closes a sad chapter in the history of Rwanda and allows the country to move on".