The Education Bureau said classes at all day schools – including kindergartens, childcare centres, as well as primary, secondary and special schools – will be suspended on Friday to ensure the safety of pupils with severe weather likely to continue.

Classes at all Thursday afternoon schools would be suspended, while morning classes and whole-day schools should continue, as heavy rain lashed the SAR.

The observatory downgraded the red rainstorm warning to an amber alert on Thursday, about an hour after the higher signal was issued.

However, the forecaster warned that heavy downpours would persist as it issued the amber signal at 10.40am, meaning rain exceeding 30 millimetres in an hour "has fallen or is expected to fall generally" over Hong Kong.

"There will be flooding in some low-lying and poorly drained areas," it said.

"People who are likely to be affected should take necessary precautions to reduce their exposure to risk posed by the heavy rain and flooding.

"Heavy rain may bring about flash floods. People should stay away from watercourses. People who are likely to be affected by flooding should take necessary precautions to avoid losses."

Officials said the decision to cancel classes on Friday was made after taking into account the fact that schools have begun or will soon begin their summer holidays and class suspensions will have a relatively minimal impact.

Parents who need to register their children with new secondary schools on Friday will have to wait until next week.

The Transport Department said it would, depending on actual traffic conditions, coordinate with public transport operators to make adjustments and arrange for emergency services.

There were two incidences of flooding along San Tin Highway as of 10am, according to the Drainage Services Department, which also deployed some 100 emergency response teams across the city.

The observatory first issued the amber rainstorm warning at 8.35am, before upgrading it to red an hour later.

The amber signal was also issued on Wednesday night and later replaced by a red signal before midnight. All warnings were cancelled at 1.40am on Thursday.

The alerts came as the territory braced for tropical storm Danas, which moved southwest across eastern Guangdong.

"Under the influence of the remnant of Danas and the active southwest monsoon, there are heavy showers and squally thunderstorms over the coast of southern China and the northern part of the South China Sea," the forecaster said.

"Locally, heavy showers this morning brought about 50 millimetres of rainfall to many places, and rainfall even exceeded 70 millimetres over Lamma Island and the southern part of Lantau Island."