The FNL launched a major offensive on Bujumbura and its outskirts on April 17, sparking intense clashes with the army in which more than 100 have been killed, including many civilians.
Habimana could not confirm the loss of 50 fighters in fighting on Wednesday.
But Burundi's army said on Thursday it had killed 50 fighters from the country's last active guerrilla group in clashes outside Bujumbura.
Colonel Adolphe Manirakiza, the army spokesman, said: "The FNL ambushed our troops on patrol, the army then entered into heavy battle with the insurgents ... two soldiers were also killed."
Habimana said: "Those who died and were captured are Burundians. The army shouldn't be rejoicing so much at a time when everybody, including the international community, is seeking to rekindle peace efforts in our country."
According to diplomatic sources, the FNL gas between 3,000 and 3,500 fighters.
A ceasefire agreement was signed between the FNL, the country's last rebel group, and the government in September 2006 but its implementation has stumbled.
An estimated 300,000 people have been killed in Burundi, one of the world's least developed countries, since the start of the civil war in 1993.
The Wednesday night battle in the FNL stronghold of Kabezi, 20km south of Bujumbura, brings the death toll since renewed violence broke out in April to 103.