Tirso Alcantara, commander of the New People’s Army, was captured late Tuesday after police and military intelligence tracked him to a hideout in Lucena city, 100 kilometres south of Manila.
In a brief exchange of fire Alcantata sustained a gunshot wound to his buttocks.
It is feared the incident could affect planned negotiations in the Norwegian capital Oslo between NPA rebel leaders and the government.
The 4,700-strong NPA is the armed unit of the Philippines’ Communist Party which has been waging a Maoist rebellion since 1969, leaving thousands dead.
Communist Party leaders have demanded that Alcantara be released before talks begin, according to Manila’s chief peace negotiator.