Muslim rebel positions were shelled by Philippine troops and fired on by helicopters overnight on the southern island of Jolo.
The attacks came after a day of fighting in which at least 54 people, including 26 troops, were killed.
The clashes, which broke out yesterday morning, were the heaviest in the volatile Philippine south for almost three years.
The military said it suspended operations at daybreak today following a request from the provincial governor.
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The military said the rebels were from the Abu Sayyaf, which is linked to al-Qaeda, but the Moro National Liberation Front, which signed a peace deal with the government in 1996, said its forces were involved.