Both cities raised a Typhoon 8 signal - the third-highest warning level - early Sunday as severe tropical storm 'Pakhar' made landfall in the region, where emergency workers were still battling to repair Wednesday's damage.
A total of 206 flights were cancelled and another 471 delayed because of the latest storm, while 44 flights had to divert, Hong Kong's Airport Authority said. Cathay Pacific, the city's flagship, said "cancellations, diversions and severe delays" were expected.
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All ferry services in Hong Kong were suspended until the storm warning was lowered in both cities in the early afternoon. Dozens of trees weakened by Wednesday's typhoon were brought down by the latest storm.
No deaths were reported on Sunday but Hong Kong hospital officials said 62 people were injured.
A Chinese cargo ship was sinking east of Hong Kong Sunday morning but all 11 crew members were rescued, the government flying service said.
Pakhar brought winds of up to 130 kilo metres per hour to Hong Kong. Sunday is a holiday but on a working day the Typhoon 8 signal would have meant the shutdown of the stock market, schools and businesses.
In Macau authorities issued fresh flooding warnings as shops that were battered Wednesday remained closed on Sunday morning. Traffic lights stayed blacked out with power yet to return to parts of the city. The water supply has been restored, a Macau government statement said Sunday, but buildings with damaged pumps still lack water.
"This is tough but there is nothing we can do," said shopowner Leung Chin-pang, who has been without water since the first storm hit.
Pakhar - named after a freshwater fish in the lower Mekong river - arrived as worst-hit Macau was still picking up the pieces following Typhoon Hato, the city's strongest typhoon in 53 years according to its government.
Hato, which triggered the most severe Typhoon 10 warning, ripped through the gambling hub Wednesday, plunging casinos into darkness and causing destructive floods.
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The official death toll in Macau reached 10, as the government of the semi-autonomous Chinese city faced recriminations over its lack of preparedness.
A further eight people are known to have died from Typhoon Hato in the neighbouring mainland Chinese province of Guangdong, which Pakhar also reached mid-morning Sunday. Dozens of visitors had returned to the main tourist attraction of Senado Square in Macau on Sunday as the clean-up progressed.
Streets appeared cleaner after local residents of all ages and around 1,000 troops from the Chinese People's Liberation Army Macau garrison worked to clear piles of debris blocking the streets.
Four Hong Kong journalists covering the impact of the typhoon were barred entry into Macau Saturday on the grounds that they "threatened the stability of internal security", according to the Hong Kong Journalists Association. The group in a statement expressed "deep regret" over the incident and urged Macau's authorities to respect press freedom.
Summer is typhoon season for the region including Hong Kong, which can experience storms of such severity that the entire city shuts down.
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