The raid on the camp near the town of Valencia was launched following a tip-off, army spokesman Major Michelle Anayron told reporters.
He said five teams of soldiers had taken part in the assault, backed up by helicopter gunships.
Anayron said the military had estimated about 60 fighters were hiding in the camp.
"We suspect that the camp is really important because the NPA does not want to give it up," he said.
The government's conflict with the NPA peaked in the 1980s when the group claimed around 26,000 fighters in its ranks.
The military estimates the NPA's numbers have since fallen to just above 3,000, but says they remain a potent force.
Earlier this year military officials said the communist rebellion in Mindanao had claimed more than 3,000 lives since 2001, including over 500 civilians killed in crossfire.