Speaking at the Chatham House foreign affairs think tank in London, Anders Fogh Rasmussen said Russia was trying to undermining attempts to exploit alternative energy sources such as shale gas.
"I have met allies who can report that Russia, as part of their sophisticated information and disinformation operations, engaged actively with so-called non-governmental organisations - environmental organisations working against shale gas - to maintain European dependence on imported Russian gas. That is my interpretation," he said.
Mr Rasmussen did not say what form the engagement took or whether the groups concerned were aware that they were dealing with Moscow's agents.
He said improving energy security was of the "utmost importance".