The Hong Kong Observatory issued the Red Rainstorm Warning at 9.50pm on Thursday, saying heavy rain has fallen or is expected to fall over Hong Kong.
The forecaster said rain is particularly heavy in Tai Po and the North District, with more than 70 millimetres of hourly rainfall expected.
It called on members of the public to be on the alert and report any street flooding.
"Further heavy rain could cause, if not already caused, serious road flooding and traffic congestion and could disrupt normal school hours," the forecaster said.
"Parents, students, school authorities and school-bus drivers should listen to radio or television announcements on schools. People who have to travel should carefully consider the weather and road conditions and take necessary precautions."
The weatherman also warned of intense gusts that will continue to affect the territory, and urged people to seek shelter as soon as possible.