Five activists were taken to hospital for treatment to cuts following the confrontation, and 12 volunteers from New Zealand, Australia, China and the Philippines were arrested and charged for trespassing but later released without any bail being posted.
German Jens Loewe, 36, was badly beaten and hit on the face and head with a crowbar while he was lying on the ground, along with Filipino activist Tomas Leonar, 24, Greenpeace said.
Private security personnel at the 600-megawatt Masinloc plant, around 150 kilometres (95 miles) northwest of Manila, also fired warning shots, the activists said.
An AFP photographer at the scene said Loewe was repeatedly hit with the crowbar and was later carried away on a stretcher and rushed to a local hospital. His condition was not immediately known.
Plant personnel refused to comment when contacted.
"We were attempting to stage a peaceful protest in the Masinloc coal power plant when a number of ground personnel became very violent and began to throw stones," Greenpeace energy campaigner Red Constantino told AFP.
"Gunshots were also fired from rifles, and one of our activists was repeatedly hit on the face and rammed with a steel bar while he was immobile on the ground.
"We did not have a permit (to enter the compound) but the issue of climate change is of utmost urgency and this prompted us to enter the plant," he added.
In a statement released in Manila Thursday night Greenpeace said it will contest the legality of the charges.
The Greenpeace flagship the Rainbow Warrior is currently in the Philippines as part of a Southeast Asian tour to raise awareness about climate change.