Toomas Hendrik Ilves said cooperation between the alliance and Russia as one of it major partners was spoilt by the military conflict in Georgia in August 2008.
"The least NATO wants in order to restore confidence in its relations with Russia is that it stops bullying its neighbors," he said.
He also criticized Russia's proposal on a new security system in Europe as unconstructive.
"I think this proposal - to destroy a well functioning system and then demand that it be replaced - is not very constructive," the Estonian president said, adding that the conflict between Russia and Georgia had altered the European security system established after the cold war.
Ilves also said the current international bodies had the capacity to cope with a potential "military invasion of Europe."