The charge against the activists -- most of them foreign nationals from Britain, Argentina, Finland and other countries -- dimmed hopes that 16 others detained over the protest could be indicted on a lesser charge.
Piracy by an organised group carries a punishment of between 10 and 15 years.
A spokeswoman for the Investigative Committee declined to provide details, saying only that the activists from the group's Arctic Sunrise icebreaker, placed in pre-trial detention for two months, were being charged.
Greenpeace called the accusations "extreme and disproportionate."
"This is an outrage and represents nothing less than an assault on the very principle of peaceful protest," Greenpeace International executive director Kumi Naidoo said.
"Any claim that these activists are pirates is as absurd as it is abominable. It is utterly irrational, it is designed to intimidate and silence us, but we will not be cowed."
He said the charges represented the "most serious threat" to environmental activism since the group's ship Rainbow Warrior was bombed by French special services in New Zealand in 1985.
Putin's spokesman Dmitry Peskov told AFP today that Putin had expressed his personal opinion.
"He is not an investigator, nor a prosecutor, judge or defence lawyer."
Among those already charged were a British freelance videographer and a Finnish activist, who was one of the climbers who attempted to scale a Russian oil platform.
Greenpeace says it will appeal and turn to the European Court of Human Rights.
The group has denied the charges and accused Russia of illegally boarding its ship in international waters.
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