Koinu had weakened into a severe tropical storm but still brought gale-force winds and heavy rain, the city's Observatory said. It was tracking west or west-southwest at around 10 kph (6 miles per hour) as it crossed the western coast of China's southern Guangdong province.
The bureau also issued a landslide warning with many areas of the mountainous city at risk after unusually wet weather.
Hundreds of passengers were stranded at Hong Kong's airport overnight and underground metro stations as Koinu disrupted flights and transport, public broadcaster RTHK reported.
The Airport Express train which connects the airport to the central business district stopped running while services at some metro stations were partially suspended. Services had since resumed at limited frequencies, operator MTR said.
The strong winds were expected to ease later in the day, the Observatory said, and the stock exchange is scheduled to reopen for the afternoon session.
The China Meteorological Administration said the eye of the storm was located in Taishan city in populous Guangdong province early Monday with a maximum wind speed of 28 meters (0.02 mile)per second, or around 100 kph.
Koinu is expected to approach Guangdong's western coast and then the eastern part of Hainan island with weakening intensity.
However, strong winds were forecast in several areas in the coastal southern region including around the mouth of the Pearl River and localized heavy rains in southwestern Guangdong, forecasts show.
Torrential rain early in September led to widespread flooding across the city, submerging streets, shopping malls and metro stations after typhoon Haikui made landfall in China's coastal Fujian province.