The Philippine security forces have been hunting the militant Abu Sayyaf group for two weeks in an operation launched across the southern Basilan and Jolo islands - two remote strongholds of the rebels in the mainly Catholic Asian nation.
The army soldiers were injured when clashes broke out early Saturday with up to 120 Abu Sayyaf gunmen in a remote rural village on Basilan, regional military spokesman Major Filemon Tan told reporters.
It came just a day after former missionary Rolando del Torchio - held hostage for six months by suspected Islamic militants - was found aboard a ferry docked on Jolo.
The Abu Sayyaf is a small group of Islamic militants infamous for kidnapping foreigners and demanding huge ransoms, as well as for being behind deadly bombings in the country where 80 percent of the population are Catholics.
Eighteen other foreign hostages are being held in the Philippines, most or all of them thought to be by the Abu Sayyaf.
Tan said the Basilan-based Abu Sayyaf are led by Isnilon Hapilon, one of its most senior figures who has pledged allegiance to the Islamic State fighters in Syria and Iraq, and who is also wanted by the US government for the kidnapping and murder of Americans.
Del Torchio was held on Jolo by another Abu Sayyaf unit led by Idang Susukan, Tan said.
The Abu Sayyaf was established in the early 1990s with seed money from Osama bin Laden's Al Qaeda network.
It was a radical offshoot of a Muslim separatist insurgency in the southern Philippines that has claimed more than 100,000 lives since the 1970s.
In a statement Tan added that the military "continues its intensified focused military operations in tracking down the ASG (Abu Sayyaf Group) responsible for the series of kidnappings and atrocities in the area".