The group was fined P384,000 earlier this week but blamed what it described as inaccurate navigational charts provided by the Philippine government after the 180-foot schooner ran aground at the Tubbataha Reef Marine Park on Monday.
The ship caused damage on an area of some 1,700 square feet of coral, authorities said.
Greenpeace offered a belated and unconditional apology after the ship sailed into the port of Manila to continue an island-hopping tour across the Asia-Pacific to promote climate change awareness.
"Yes, we admit we are human too. We apologize that this thing happened," Greenpeace Southeast Asia campaign manager Von Hernandez told a news conference.
He said it was Greenpeace’s understanding that "that these things happen quite frequently" at Tubbataha, a spectacular 32,000-hectare coral formation in the Sulu Sea that is listed by the UN Educational, Scientific and Cultural Organization as a world heritage site.
By paying the fine and making an act of contrition, "we hope we have set a positive example as far as this thing is concerned," Hernandez said.
Originally built in Britain in 1957 as a steam-powered fishing vessel, the Rainbow Warrior II replaced its namesake, which was sunk by French agents in 1985 in Auckland harbor on its way to block a French nuclear test in the South Pacific.
One crew member drowned and two French secret service agents were later jailed after pleading guilty to charges of manslaughter and willful damage. — AFP