However, despite the cloudy skies Beijing officials said air quality remained "fairly good", and experts predicted clear weather for the opening ceremony.
Meanwhile, China's authorities have said they are confident that all athletes and spectators will be safe, after an attack by suspected separatist Islamist militants killed 16 policemen on Monday in the western region of Xinjiang.
A spokesman for the organisers said preparations had been made to protect some 10,500 athletes from 205 countries during the Olympics.
"China has focused on strengthening security and protection around Olympic venues and at the Olympics Village, so Beijing is already prepared to respond to any threat," Beijing Games spokesman Sun Weide was quoted as saying.
Officials in the co-host city of Shanghai say all shops and businesses in the metro stations have now been closed until after the Olympic Games because of public security concerns.
The operator of the underground rail system, Shentong Metro Group, said the move would affect more than 1,000 shops, and even vending machines would be closed. It said it would not provide compensation for business owners.
Meanwhile state media reported that four pro-Tibet activists from Britain and the US had been arrested in Beijing after a brief protest close to the Olympic stadium.
Basketball star Yao Ming was mobbed by fans after his run with the torch
Students for a Free Tibet said it was behind the protest, in which members unfurled two large "Free Tibet" banners from electricity poles.
The international leg of the torch's tour earlier this year was marred by protests in several cities - including London, Paris and San Francisco.
Activists demonstrated against China's human-rights record and its handling of violent anti-Beijing protests in March in Tibet.
In other developments:
The US has complained that a co-founder of activist group Team Darfur, former Olympian Joey Cheek, had his visa revoked hours before he was due to travel to Beijing
Police banned US swimmer Amanda Beard from giving a pro-animal rights news conference inside an Olympic venue - but allowed her to protest in another location
The International Olympic Committee said it believed the Chinese authorities had done everything possible "to ensure the security and safety of everyone at the Games".
The IOC has also assured athletes that the smog which often plagues the city would not pose major health problems.
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