The Charité hospital released a statement saying "clinical evidence suggests an intoxication through a substance belonging to the group of cholinesterase inhibitors".
But doctors who treated him in Russia say the substance was not present.
Mr Navalny fell ill on an internal flight in Russia on Thursday.
Video appeared to show Mr Navalny, a dogged critic of the Kremlin, writhing in agony on the flight from Tomsk in Siberia to Moscow.
His supporters suspect poison was placed in a cup of tea he drank at the airport in Tomsk.
