The series of skirmishes occurred around several small military outposts near the rural town of Pikit between Tuesday and yesterday, local military spokesman Captain Antonio Bulao told AFP.
Nine members of the Bangsamoro Islamic Freedom Fighters were killed in the fighting, Bulao said, citing intelligence reports.
The rebel faction's spokesman, Abu Misri, confirmed that its forces were involved in the fighting, but denied that it sustained casualties.
Bulao said two soldiers were wounded in the fighting.
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Bulao accused the renegade rebels of extorting from private contractors of a government irrigation project, but Misri denied this.
Misri also said the latest flare-up of fighting was unrelated to the government's peace talks with the MILF.
"This has no relation to the peace talks. We will not sabotage them," he told AFP.
He said the rebels attacked because soldiers allegedly harassed Muslim farmers in the area, which Bulao denies.
However the BIFF have refused to abide by the ceasefire, and have staged scattered attacks on civilians and the armed forces.
President Benigno Aquino has promised to end the insurgency by the conclusion of his six-year term in 2016.
The peace talks reached a crucial stage last month after the two sides hammered out the details of a power-sharing agreement within a proposed Muslim self-rule area in the south.