MILF has maintained that the area captured by the military was in fact a Muslim settlement.
The military also claims the 30 MILF fighters were killed in the battle to capture the base, located near Guindulungan town in southern Maguindanao province.
"Based on our initial report, our troops have accounted for 30 killed rebels on the ground," Lieutenant-Colonel Jonathan Ponce, a military spokesman, said.
"We bombed their positions. We fired rockets until early this morning before soldiers entered the rebel encampment"
"We bombed their positions. We fired rockets until early this morning [Saturday] before soldiers entered the rebel encampment."
The camp is reported to have housed 20 bunkers that could accommodate about 200 fighters.
Soldiers found dozens of bodies inside concrete bunkers and discovered a large cache of weapons, munitions and explosives.
"This was also a bomb factory," Ponce said.
The military said only five of its soldiers were wounded in the heavy fighting.
MILF has been fighting the Philippine government since the early 1970s.
They had appeared on the verge of signing a formal peace deal with the government last year, until the supreme court blocked the agreement and rebel forces attacked civilian villages in response.
In a separate development in the southern Philippines, a hostage escaped from another group opposed to the government, the Abu Sayyaf.
Officials said that the woman escaped barefoot from her captors as they tried to evade a marine offensive that killed three of the kidnappers.
The Filipino woman, who was abducted by Abu Sayyaf fighters on February 3 on Basilan Island, escaped from her captors' jungle hideout and was found by villagers before dawn on Sunday in Sumisip township.
Lea Laping Patris is the latest of several hostages to escape from the Abu Sayyaf.
The allegedly al-Qaeda-linked group has been weakened by years of US-backed offensives against them, but security officials worry that kidnappings for ransom could revive the group and have been cracking down.