From Monday onwards, all kindergartens, primary and secondary schools will close when the red rainstorm warning is hoisted.
The new system, announced by the Education Department yesterday, follows criticisms by the Ombudsman that the existing system was confusing.
At present, schools close during black rainstorm warning.
Scores of parents complained last year when schools failed to close despite severe flooding.
A department spokesman said the new system takes into account the Observatory's new warning system, which uses a forecast element giving parents time to prepare.
He said schools would operate as usual under the amber signal which predicts or measures 20 millimetres of rain an hour, but would close under the red or black. The red signal will warn of rainfall exceeding 50 mm an hour and the black signal for 70 mm or above per hour.