According to the BBC, the body examined materials used inside the PS3, 360 and Wii and found that, while all three machines complied with European laws, they contained harmful materials that "needed to be replaced".
Nintendo's environment policies were "non-existent", Greenpeace added.
"Nintendo doesn't have any environmental policies, " said Zeina Al-Hajj, Greenpeace's International Toxic Campaign co-ordinator.
"We were shocked with Nintendo; it was our biggest surprise."
Nintendo is ranked at the bottom of Greenpeace's global assessment of "green" technology companies.
"Recently they added a list of certain commitments they have, which purely comply with legislation," said Ms Al-Hajj.
The organisation has called on all technology firms to take immediate action to eliminate toxic chemicals from products.