Classes of all PM schools have been suspended after the Red Rainstorm Warning Signal was issued at 10:45am on Wednesday.
All AM and whole-day schools which are in session, meanwhile, should continue until the end of school hours.
The Hong Kong Observatory said heavy rain has fallen or is expected to fall generally over Hong Kong, exceeding 50 millimetres in an hour, and is likely to continue.
It called on parents, students, school authorities and school-bus drivers to keep tabs on radio or television announcements, saying serious road flooding and traffic congestion could disrupt normal school hours.
People who need to travel have also been advised to consider the weather and road conditions, and take necessary precautions.
Meanwhile, the weatherman said a waterspout was spotted at Cheung Chau at around 10:30am.