At least one smoke bomb was let off after between 60 and 100 students managed to enter the building on Tuesday night although they did not get into the room itself, media reports said.
Photographs showed a plume of red smoke inside the building and the presence of police wearing helmets and body protectors.
Outside, students held up banners with slogans such as ‘chase Blatter away’.
Public transport was disrupted for around two hours in the region around the ETH university although no arrests or injuries were reported. Blatter, 78, is planning to stand for a fifth term as FIFA president in next year’s election. His lecture was titled ‘Football as a school of life’.