The National Liberation Forces (FNL) launched their assault on government forces around 04:00 (02:00 GMT) near Minago and Rutwenzi, both in Bururi province, according to provincial governor Anicet Niyongabo.
"Fighting has stopped in the first location but was continuing at nightfall in the second," he said.
Minago lies about 60km south of the capital, Bujumbura, and Rutwenzi is about 50km southwest of the capital.
"It's the first time the FNL have attacked so far south of Burundi since the start of the war," the governor added.
Reasons for raid
The FNL – the last Hutu rebel group to continue the civil war - refuses to negotiate with the government, claiming it has no legitimacy.
Their forces admit carrying out the attack.
FNL spokesman Pasteur Habimana said the raid show “that the FNL is not a small movement, that it can hit anywhere it wants outside Bujumbura”.
"We have shown up those who said the FDD (the Forces for the Defence of Democracy) was the main rebel movement, that peace would come from their signing a peace accord," with the government, Habimana said.
The FDD signed a comprehensive deal with the administration on 16 November and its leaders have now joined an enlarged government while its fighters are set to make up 40% of a revamped army.
However, Niyongabo said the army was using heavy artillery in Rutwenzi to dislodge the rebels.
"There have been no casualties as far as we know even though tens of thousands of civilians have fled the area," he said.
More than 300,000 people have been killed in Burundi's civil war, most of them civilians.