Niyonkuru,54, was shot dead by unknown gunmen in the early hours of Sunday in the capital city of Bujumbura, the country’s police authorities said.
He was appointed minister by President Pierre Nkurunziza in August 2015 after a long time in banking.
At least 500 people have been killed and 300,000 have fled the country since political unrest began in April 2015.
He was killed shortly after midnight, according to a tweet sent by police spokesman Pierre Nkurikiye.
The murder, the first of a serving government minister since Burundi sank into turmoil over President Pierre Nkurunziza’s controversial bid for a third term , came after months of relative calm.
“Minister of water and environment killed by a criminal with a gun on his way home to Rohero, around 00:45,” Nkurikiye wrote four hours after the incident.
He added that a woman had been arrested following the “assassination”.
Also on Twitter, Nkurunziza offered his condolences “to the family and all Burundians” vowing the crime would be punished.
Niyonkuru was born on 20 July 1962 in Gashingwa in the province of Muramvya. He attended the University of Burundi from 1987 to 1991 in the Faculty of Economic and Administrative Sciences.
He was elected Senator of the electoral district of Muramvya for the 2015-2020 term.
From 2 January 1992 to 24 August 2015, Niyonkuru was deputy director of the Bank of the Republic of Burundi (BRB).
Until his appointment as minister, he was a member of the Monetary Policy Committee of the Bank of the Republic of Burundi and a member of the National Committee for Development and Implementation of the Development Plan. Financial Market in Burundi.
