It the first significant fighting reported between the two sides since Islamist and Tuareg rebels seized control of the north of the country last April.
The Islamists had reportedly tried to make an advance into the government-controlled south.
It is not clear whether there were any casualties.
The army used artillery against the Islamist fighters in the village of Gnimignama, 30km (19 miles) from army positions, according to army sources.