Ahmed Mismari, the spokesperson for the Libyan National Army (LNA) that controls eastern Libya, said in a televised news conference that the disaster came after dams above Derna had collapsed, "sweeping whole neighbourhoods with their residents into the sea".
Mismari put the number of missing at 5,000-6,000, Reuters reported.
Earlier on Monday, the head of the Red Crescent aid group in the region had said Derna's death toll was at 150 and expected to hit 250. Reuters could not immediately verify either figure.
Libya is politically divided between east and west and public services have crumbled since a 2011 NATO-backed uprising that prompted years of conflict. The internationally recognised government in Tripoli does not control eastern areas.
In Tripoli, the three-person Presidential Council which functions as head of state in the divided country asked the international community to help. "We call on brotherly and friendly countries and international organisations to provide assistance," it said.
Osama Hamad, the head of a parallel eastern-based administration, told local television that more than 2,000 were dead and thousands more missing.
After pummelling Greece last week, Storm Daniel swept in over the Mediterranean on Sunday, swamping roads and destroying buildings in Derna, and hitting other settlements along the coast, including Libya's second-biggest city of Benghazi.
Videos of Derna showed a wide torrent running through the city centre where a far narrower waterway had previously flowed. Ruined buildings stood on either side.
Eastern Libya's Almostkbal TV broadcast footage that showed people stranded on the roofs of their vehicles calling for help and waters washing away cars.
"The missing are in the thousands, and the dead exceed 2,000," Osama Hamad told al-Masar TV. "Entire neighbourhoods in Derna have disappeared, along with their residents ... swept away by water."
Mismari said seven members of the LNA had died in the flood.
MNA/PR
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