The Philippine military, police and the human rights commission said on Tuesday that they would separately investigate the deaths.
The latest clash broke a week-long lull in fighting that first erupted last month after a proposed peace deal between the government and the separatist Moro Islamic Liberation Front was aborted.
Scores of civilians have been killed and more than half a million people have lost their homes and livelihoods since.
Orlando De Guzman, reporting for Al Jazeera from Cotabato province which borders Datu Piang, said entire villages had become "free-fire zones" as the military stepped up its campaign against the separatists, who have pillaged several towns and villages themselves.
With mounting civilian casualties and a growing refugee crisis, the military operations may be turning the people in the south against the government, our correspondent said.
Leila de Lima, head of the independent Commission on Human Rights, said the displacement of communities as a result of the clashes was "a national concern of crisis proportion".
And the International Red Cross deputy director of operations, Dominik Stillhart, has appealed to separatist fighters and the military not to harm civilians as they battle each other in the worst fighting in the southern Philippines since 2003.