January 19, 2017 0431 GMT
Emmanuel Niyonkuru, 54, was attacked as he traveled home in the Central African nation's capital Bujumbura, police spokesman Pierre Nkurikiye said in a tweet, Reuters reported.
Violent protests erupted early in 2015 after President Pierre Nkurunziza said he would seek a third term – a move opponents said violated the constitution and a peace deal that ended an ethnically charged civil war.
At least 450 people have died in clashes between protesters and security forces, tit-for-tat killings and a failed coup, stoking fears of wider unrest in a region still haunted by the 1994 genocide in neighboring Rwanda.
"The minister of water and environment was shot ... as he was getting home," police spokesman Nkurikiye said. A woman with the minister had been arrested for questioning, he added.
President Nkurunziza said on Twitter the minister had been assassinated and offered condolences "to the family and all Burundians".
Nkurunziza went on to win reelection in July 2015 in a poll largely boycotted by the opposition.