Emmanuel Niyonkuru, 54, the country's water, environment and planning minister, was shot dead shortly after midnight on New Years Eve in the most high-profile killing since Burundi's political crisis began nearly two years ago.

Police were quick to term the killing an "assassination" although the motive for the attack was not immediately clear.

Prosecutor general Sylvestre Nyandwi told journalists that the minister had been shot in the head as he returned home in the capital Bujumbura.

"After this foul act, investigations began quickly and six suspected perpetrators were apprehended, including four men and two women," he said.

Nyandwi said investigations were still ongoing and did not reveal the identities of those arrested nor their alleged motives.

Niyonkuru is the first cabinet minister to be killed but other senior regime figures have been targeted since the crisis erupted over President Pierre Nkurunziza's bid to run for a third term in April 2015.

General Adolphe Nshimirimana, considered Nkurunziza's right-hand man, was killed in August 2015.

Almost a year later former government minister and spokesperson Hafsa Mossi was killed by gunmen in her car.

Other attacks have failed, with senior presidential advisor Willy Nyamitwe, a spokesperson widely regarded as the public face of the government, escaping an ambush by a group of gunmen as he returned to his Bujumbura home in November.

Burundi has commonly blamed neighbouring Rwanda for the attacks.

At least 500 people have been killed and 300 000 have fled the country since the unrest began as protesters - and then military coup-plotters - fought against Nkurunziza's third mandate.

UN and NGO human rights reports have raised fears that Burundi's political crisis might take on an ethnic dimension, warning of the potential for genocide.