"I returned from Derna. It is very disastrous. Bodies are lying everywhere - in the sea, in the valleys, under the buildings," Hichem Chkiouat, minister of civil aviation and member of the emergency committee, told Reuters by phone.
"The number of bodies recovered in Derna is more than 1000," he said. He expected the final toll would be "really, really big".
"I am not exaggerating when I say that 25 per cent of the city has disappeared. Many, many buildings have collapsed."
Officials in the administration that runs the eastern part of the divided country said on Monday at least 2000 people had been killed by the floods, though it was not immediately clear what that estimate was based on.
Officials said thousands more were missing from the flood, which they said had swept away entire neighbourhoods after dams burst above the city.
A video shared on Facebook, which Reuters could not independently verify, appeared to show dozens of bodies covered in blankets on the pavements in Derna.
An emergency medical supply plane carrying 14 tonnes of supplies, medications, equipment, body bags and 87 medical and paramedic personnel is heading to Benghazi to support the areas affected by the flood, the head of Libya's Government of National Unity, Abdulhamid al-Dbeibah, said on Tuesday.
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.
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.
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