"The European Council condemns the attempt to assassinate Navalny with a military poisonous nerve-paralyzing substance from the Novichok group," the president said in a comment sent to BNS on Friday.
"The use of a chemical weapon is a gross violation of international law," he added.
Nauseda is also calling on Russian government institutions to "fully cooperate" with the Organization for the Prohibition of Chemical Weapons (OPCW) for responsible people be held accountable.
The Lithuanian leader says the European Council is set to once again discuss the Navalny issue on October 15-16.
Nauseda is currently attending a European summit in Brussels.