The Hong Kong Observatory issued the Amber Rainstorm Warning Signal at 4.08am on Friday.
It means that heavy rain has fallen or is expected to fall over Hong Kong, exceeding 30mm in an hour, and is likely to continue.
There will be flooding in some low-lying and poorly drained areas, the observatory said, adding people who are likely to be affected should take precautions to reduce their exposure to risk posed by heavy rain and flooding.
It also warned heavy rain may cause flash floods, and urged people to stay away from watercourses.