The Observatory issued the Red Rainstorm Warning Signal at 12.15pm on Friday as heavy rain lashed the city.
It replaced the Amber Rainstorm Warning which had come into force less than half an hour earlier.
The Observatory said the Red Rainstorm Warning suggested that heavy rain has fallen or is expected to fall generally over Hong Kong, exceeding 50 millimetres an hour.
It also warned of possible floods and urged people to stay away from watercourses.
The Education Bureau said students of PM schools do not have to attend school in the afternoon due to the rainstorm.
Schools that are in session should continue until the end of school hours, it added.
