"The toll from the earthquake is 2,189," the agency said on Twitter.
More than 12,260 people were injured when the quake hit the southwestern part of Haiti on Saturday, about 100 miles (160 kilometers) to the west of the capital Port-au-Prince, according to the updated toll.
The civil protection agency added that 332 people have been reported missing and rescue operations were ongoing.
Tens of thousands of buildings were destroyed and damaged in the impoverished country still recovering from another devastating earthquake in 2010.
Haiti has also been beleaguered by gang violence, Covid-19, and political chaos, which spiked last month after the assassination of president Jovenel Moise.
The government has declared a month-long state of emergency in the four provinces affected by the quake.
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