The Hong Kong Observatory issued the red rainstorm warning on Tuesday evening as heavy downpours hit the territory.
The warning, issued at 7.15pm, means that heavy rain has fallen or is expected to fall generally over Hong Kong, exceeding 50 millimetres in an hour, and is likely to continue, the Observatory said.
Hong Kong Island was the worst-hit area with more than 40mm of rainfall recorded between 6pm and 7pm.
The Observatory predicted heavy showers would continue tomorrow and could be heavy at times.
It warned that heavy rain could cause serious road flooding and traffic congestion. It also urged people to stay away from watercourses and residents living in close proximity to rivers to consider evacuation if their homes might become flooded.