The toll was likely to rise, added Toussaint Kongo-Doudou, spokesman for the United Nations Stabilisation Mission in Haiti (MINUSTAH).
Eighty percent of the city of Gonaives, about 110km north of the Haitian capital Port au Prince, is flooded, he said on Sunday.
Two days of steady rain sent torrents down the mountains of northern Haiti, causing a river to burst its banks, officials said.
A government delegation led by Prime Minister Gerard Latortue earlier gave the toll as 30 after returning from a tour of severely flooded areas in the north of the impoverished country.
At least eight people have been
killed in the Dominican Republic
UN peacekeepers were deployed to help survivors. They made 12 helicopter flights over Gonaives on Sunday and transported water and medicine to the region on Monday.
The World Food Programme is also planning to ship food by truck to troubled areas, Kongo-Doudou said.
The hospital and police station are among the buildings flooded in Gonaives, which in many places is under 3m of water, the UN spokesman said.
Two medical teams from Argentina and a team from Medecins San Frontieres (Doctors without Borders) will also depart Port au Prince for northern Haiti on Tuesday.
The disaster came four months after floods killed more than 3000 people in the border area between Haiti and the Dominican Republic.
At its strongest, Jeanne killed at least eight people in the Dominican Republic and Puerto Rico.
In the Bahamas, the government called off all warnings on Sunday as Jeanne took a north-westerly turn out into the sea.
The storm comes in the wake of Hurricane Ivan, which killed more than 100 people and caused widespread damage in the Caribbean and the southern US last week.