The group used inflatable boats to access the vessel and painted "Australia Pushing Coal Export" in 2 metre high letters along the side.
They were arrested by water police, had their boats seized and will appear in the Newcastle Court on September 11.
A male member of the group was also charged with dangerous navigation.
Greenpeace energy campaigner Ben Pearson said the peaceful protest was intended to highlight Australia's role in the booming coal export industry and reluctance to sign the Kyoto Protocol.
"Real action on climate change means moving away from coal and shifting to clean, renewable energy and we don't have the luxury of time for expensive talkfests that have no concrete outcomes," Pearson said.
During APEC week Australia will export more than four million tonnes of coal, resulting in more than 11 million tonnes of CO2 emissions, equivalent to the annual emissions from 800,000 average Australian households, according to Greenpeace.
