Greenpeace said in a statement today that the accusation was a smear.
It said there was a strict policy against recreational drugs on Greenpeace ships, and any claim that something other than medical supplies were found should be regarded with great suspicion.
"The ship was first searched by Russian officers weeks ago. They scoured every corner of it, so we assume this announcement is designed to deflect attention from the growing global outrage over the continued imprisonment of the detainees.
"Any claim that illegal drugs were found is a smear, it's a fabrication, pure and simple."
Greenpeace said the Dutch-flagged ship was subject to Dutch law, under which it was illegal to sail without the right medical supplies.
"The ship had on board a fully qualified doctor with over 10 years' experience in Russian hospitals. Certain medical supplies are kept in a safe that only the captain and the doctor have access to.
"We know that the safe was broken into by the Russian authorities during the searching of the ship. We can assume these are the medical supplies that the Russian security services are referring to."
Greenpeace said the ship was searched with a sniffer dog by Norwegian authorities before embarking for the Arctic.
"The laws in Norway are amongst the strictest in the world, and nothing was found because nothing illegal was on the ship."
Yesterday, a Russian court in Murmansk rejected bail applications for two Greenpeace activists and a freelance photographer arrested on piracy charges.
A further 27 bail hearings are to be heard later this week.