Gunmen in Burundi shot dead a high-ranking military officer seen as a critic of the regime, a witness and an army spokesman told AFP on Thursday.

Lieutenant-Colonel Emmanuel Buzubona died on his way home on Wednesday along with his driver when he was attacked by three men armed with rifles and grenades, the witness told AFP on condition of anonymity.

The killing comes amid turmoil in the country since President Pierre Nkurunziza decided to run for a third term, which he went on to win in July 2015, with violence leaving hundreds dead.

Suspected of forging an alliance with insurgents opposed to Nkurunziza's bid for a third term, Buzubona was arrested in December 2015 by the national intelligence service, which operates on the direct orders of the president.

He was released six days later, a security source told AFP.

Army spokesman Colonel Gaspard Baratuza confirmed what the witness saw, adding that the attackers first shot Buzubona and then hurled a grenade at him.

"A police inquiry is under way to try to find the assassins," he said.

Buzubona, Burundi's former deputy military intelligence chief, had been on leave since his return from a mission in Tanzania six months ago, another high-ranking military officer told AFP on condition of anonymity.

There has been no claim of responsibility for the latest killing, but supporters and opponents of Nkurunziza traded accusations on social media networks.

Supporters of the regime accuse soldiers of the former Tutsi army of shooting dead the Hutu officer.

Opponents however say the officer was killed because he was hostile to the government.

- Deadly shootout -

In a separate incident in southern Burundi, two civilians were killed and two others wounded in the crossfire during a shootout on Wednesday between troops and "armed criminals", a police spokesman said Thursday, using a term often used by the government to refer to rebels.

"A military patrol was sent to Kivumu hill where people had reported the presence of armed criminals in a bar. There was an exchange of fire and four residents present at the scene were injured, two of who died from their wounds," deputy police spokesman Moise Nkurunziza said.

Witnesses say police had initially arrested all the men at the bar.

"They let us go, warning us against helping the rebels who had been reported to be in the area, but they took with them eight young men," a resident of Mugumba told AFP on condition of anonymity.

Located some 90 kilometres (60 miles) south of the capital Bujumbura, Mugumba has seen some of Burundi's most frequent clashes between government forces and armed rebels.

Four ruling party militants were killed in two incidents on Saturday, police says.

Violence over the past year has left more than 400 people dead and forced more than 250,000 people to flee Burundi, and watchdogs have repeatedly sounded the alarm.