The Observatory has issued the second black rainstorm warning within a week, warning that heavy downpours might persist.
The rainstorm alert was upgraded to the highest level at 9.45 am on Saturday.
"This means that heavy rain has fallen or is expected to fall generally over Hong Kong, exceeding 70 millimetres in an hour, and is likely to continue," the Observatory said.
"Because of seriously flooded roads and inclement weather conditions, you are advised to take shelter in a safe place and stay there... Heavy rain will bring flash floods, and flooding is occurring or is expected to occur in watercourses."
The forecaster first issued the amber warning at 6.50 am, before raising it to the red signal at 9.10 am.
Earlier on Tuesday, Hong Kong's first black rainstorm signal of the year was up for nearly two hours.