Emmanuel Niyonkuru, 54, was attacked as he travelled home in the central African nation’s capital Bujumbura, police spokesman Pierre Nkurikiye said in a tweet.
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 neighbouring 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.
Hundreds of people, including high-ranking army officials, have been killed in unrest since President Pierre Nkurunziza ran for a third term in 2015, a move which opponents said was unconstitutional. But this is the first time a serving government minister has been killed.
For months the country had been relatively calm.