Swathes of northern China endured deadly rains and floods since last week that forced the evacuation of tens of thousands.
The capital's rural suburbs were hardest hit, officials said, raising the toll from the previously reported 30 announced on Tuesday.
"As of midday on July 31, some 44 people have died and nine are still missing as a result of the disasters across the whole of Beijing," top city official Xia Linmao told a news conference.
"Between July 23 and 29, Beijing suffered extreme rainfall," he said, adding they had caused "significant casualties and (other) losses".
Out of those deaths, 31 took place at an "elderly care centre" in the town of Taishitun in the northeast of the city, Xia said.
Among those still missing are local officials working on search and rescue, he added.
"On behalf of the municipal party committee and the city government, I would like to express deep mourning for those who have regrettably lost their lives, and profound condolences to their relatives," he said.
Xia vowed to "learn profound lessons" from the disaster.
"Our ability to forecast and warn of extreme weather is insufficient, and disaster prevention and mitigation plans have not been fully developed. There are still shortcomings in the construction of infrastructure in mountainous areas," he said.
Yu Weiguo, ruling Communist Party boss in the hard-hit Miyun district, also admitted there had been "gaps" in readiness.
"Our knowledge of extreme weather was lacking. This tragic lesson has warned us that putting the people first, putting human life first, is more than a slogan," he said.
Natural disasters are common across China, particularly in the summer when some regions experience heavy rain while others bake in searing heat.
China is the world's biggest emitter of the greenhouse gases that drive climate change and contribute to making extreme weather more frequent and intense.
But it is also a global renewable energy powerhouse that aims to make its massive economy carbon-neutral by 2060.
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