The category one storm packing gusts of up to 120kmh struck late on Tuesday, destroying several shanty towns on the coast near Manila, and cutting power on the main island of Luzon.
Officials are concerned the death toll may rise and are still trying to determine the full extent of the damage with many communications systems brought down by the storm.
In Manila the city's overhead railway system was also shut down due to the power outage that brought much of the city to a standstill.
"The wind howled like a child screaming... it was so strong, our houseboat nearly got flipped over," said Rigor Sambol, 52, who lives in a coastal shanty area near Manila.
"I had to take the children one by one to a nearby gym where they spent the evening on the cold floor," he told the AFP news agency.
"I nearly lost my three-year-old when he fell into the water because he got knocked down by the strong winds."
|Shanty towns around the capital were badly damaged [AFP]|
By Wednesday morning the storm had blown past Luzon and into the South China Sea, but some international flights in and out of Manila were still cancelled while others were delayed.
Classes at many schools were suspended.
The Philippines lies in the so-called typhoon belt of the western Pacific and is swept by up to 20 cyclones a year, killing hundreds of people.
Conson was the first of the storm of the 2010 season, and its ferocity took the 12 million residents of Manila by surprise.
On Wednesday the country's newly-installed president, Benigno Aquino, criticised the state weather service for not giving adequate warning to Manila residents that Conson would hit the city.
"This is not acceptable," Aquino told red-faced weather service officials at an emergency meeting of rescue agencies.
"We rely on you to tell us where the potential problems are."
Many Manila residents had apparently been assured by forecasters' bulletins that Conson would hit the northern provinces instead of Manila.
However, the weather service failed to mention that the typhoon had a wide radius of 300km.