The avalanche occurred on Monday morning at the Nasu Onsen family ski resort near the town of Nasu in the Tochigi prefecture.
The six people were found with no vital signs, and three others were missing, according to Japan's Kyodo news agency.
About 70 people including students and teachers from several schools are said to have been in the area at the time.
Local media reports said they were taking mountain climbing lessons.
Rescue efforts are under way, with officials investigating whether more people are injured or missing.