According to the United Nations, 500 people were killed in city of Gonaives and another 56 people died in the nearby town of Port-de-Paix.
There is particular concern about the island of La Tortue, which is said to be barely visible under the water.
The storm also reportedly killed 11 people in the Dominican Republic, and has now moved north into the Atlantic.
Two days of steady rain sent torrents down the mountains of northern Haiti, causing a river to burst its banks, officials said.
Haiti's interim Prime Minister Gerard Latortue called for international help, describing the flooded area as "a vast sea".
Mr Latortue said 80,000 people were without food and water in Gonaives, the biggest city in the area.
People were left huddled on rooftops, while roads around the city were transformed into rivers.
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