Two pro-independence groups said on Tuesday that students were distributing flyers and stickers at 12 of the SAR's schools to promote the idea of Hong Kong breaking away from China.
Studentlocalism and the Hong Kong National Front said on their social media accounts that they had organised the leaflet distribution and are hoping to promote the idea of independence to students at all of the city's secondary schools and tertiary institutions.
They accuse Beijing and SAR officials of "poisoning" local youngsters with national education and by introducing Mandarin as the medium of instruction in schools.
A photo of a flyer on their websites shows a slogan which says "the only way to protect Hong Kong is independence".
Both groups have several thousand followers on their Facebook accounts, while the front's Instagram talks of "armed resistance against the Communist China regime".
In response to the flyers, the Education Bureau said calls for independence violate the "One Country, Two Systems" principle and the Basic Law, and schools should have enough experience in dealing with such political issues.
Independence banners and posters went up at the city's universities at the start of the current academic year, sparking confrontations on campuses between opponents and those insisting it was a matter of freedom of speech.
The vice-chancellors of 10 universities issued a joint statement in the middle of September saying "we treasure freedom of expression but we condemn its recent abuses".