Vladimir Markin, the investigative committee spokesman, said the protest, which occurred last week at an Arctic oil rig owned by the state-controlled gas company, constituted piracy.
Russian border guards seized the organization's ship Thursday, after detaining two activists for climbing the rig to protest drilling.
Activists told RIA Novosti the protest was peaceful and they were unarmed.
Border guards towed the ship to land, and authorities said they will question the activists on board and detain any suspects.
Greenpeace said the allegations are unfounded and don't comply with Russian law on piracy.
"Article 227 of the Criminal Code on Piracy has three qualifying features: the capture of a vessel with the use of violence, for the purpose of appropriating someone else's property," Mikhail Kreindlin, a Greenpeace Russia campaigner, told RIA Novosti.
He said none of those conditions was met.