The Black Rainstorm Warning was issued at 6.35pm as it came into effect for the second time on Thursday.
The Observatory said it means heavy rain has fallen or is expected to fall generally over Hong Kong, surpassing 70 millimetres in an hour, and is likely to continue.
Members of the public are urged to take shelter in a safe place.
The black signal was in force from 12.55pm to 3.05pm earlier in the day.
