More than 2000 people are feared dead in eastern Libya, a leader says, after a huge storm swept through the north African nation, with floods wiping out buildings and causing roads to collapse.

Storm Daniel, a major Mediterranean weather system, had already smashed Greece, Turkey and Bulgaria before bringing “catastrophic” flooding to Libya.

A Libyan government official said people had been swept away in raging torrents, and whole neighbourhoods had disappeared.

The potential death toll was announced by Osama Hamad, prime minister of Libya’s eastern parliament-backed government, and has been circulated by Libya’s state news agency.

“Osama Hamad said in press statements that residential neighbourhoods disappeared after the torrents swept them into the sea along with thousands of their residents, and the situation is catastrophic and unprecedented in Libya,” Libya News Agency reported.

Mr Hamad told al-Masar TV: “The missing are in the thousands, and the dead exceed 2,000. Entire neighbourhoods in Derna have disappeared, along with their residents…swept away by water.”

Reuters has not been able to independently verify the numbers. Mr Hamad’s government in eastern Libya is not internationally recognised.

The Red Crescent humanitarian organisation told Reuters the death toll in one city of Derna was “at least 150 deaths” after the collapse of buildings.

“We expect the death toll to rise to 250. The situation is very catastrophic,” the Red Crescent’s Kais Fhakeri said.

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Footage on social media showed nothing but debris where housing blocks once stood, seemingly washed away when deep water ripped through the city of Derna.

People were stranded on the roofs of submerged vehicles while desperately trying get help.

Storm Daniel hit the cities of Benghazi, Sousse, Al Bayda, Al-Marj and Derna on Sunday and Monday (local time).

Derna resident Saleh al-Obaidi said houses in a valley near the city had collapsed.

“People were asleep and woke up and found their homes surrounded by water,” he told Reuters.

Ahmed Mohamed, another resident, said: “We were asleep, and when we woke up, we found water besieging the house. We are inside and trying to get out.”

Libya’s eastern-based parliament declared three days of mourning.

Storm Daniel causes flooding in the city of Marj, Libya. Photo: AAP

Search-and-rescue operations were ongoing, witnesses said. Authorities declared a state of extreme emergency, closing schools and stores and imposing a curfew.

Four major oil ports in Libya, Ras Lanuf, Zueitina, Brega and Es Sidra, were closed from Saturday evening for three days, two oil engineers told Reuters.

The prime minister of the interim government in Tripoli, Abdulhamid Dbeiba, said he had directed all state agencies to “immediately deal” with the damage and floods in eastern cities.

The United Nations in Libya said it was following the storm closely and would “provide urgent relief assistance in support of response efforts at local and national levels”.