About 3,000 people were displaced in Albayda, 1,000 in Almkheley and 2,085 in Benghazi, the UN agency said on X, formerly Twitter.
It added that the number of deaths was currently unverified.
The IOM and its partners were immediately sending “NFIs [non-food-items], medicines, search-and-rescue equipment and personnel to the affected areas”, it said.
Hichem Abu Chkiouat, Minister of Civil Aviation in the administration that runs eastern Libya, said on Wednesday that more than 5,300 bodies have been counted in Derna. That toll is expected to increase significantly.
“The sea is constantly dumping dozens of bodies”, Mr Abu Chkiouat told Reuters, adding that reconstruction would cost billions of dollars.
Storm Daniel caused deadly flooding in many eastern towns but Derna was hit the hardest.
As the storm pounded the coast on Sunday night, Derna residents said they heard loud explosions when the dams outside the city collapsed.
Floodwaters washed down Wadi Derna, a river running from the mountains through the city and into the sea.
The devastation is an indication of the storm’s intensity, but also Libya's vulnerability. The country is divided by rival governments, one in the east and the other in the west, and the result in many areas has been neglect of infrastructure.
The floods damaged or destroyed many access roads to Derna, hindering the arrival of international rescue teams and humanitarian assistance to tens of thousands of people whose homes were destroyed or damaged.
Local emergency responders, including troops, government workers, volunteers and residents, continued digging through rubble looking for victims. They also used inflatable boats and helicopters to retrieve bodies from the water and inaccessible areas.
Bulldozers have worked over the past two days to fix and clear roads to allow the delivery of humanitarian aid and heavy equipment urgently needed for the search-and-rescue operations.
The city is 250km east of Benghazi, where international aid started to arrive on Tuesday.
Mohammed Abu-Lamousha, a spokesman for the Interior Ministry in the eastern government, on Tuesday put the death toll in Derna at more than 5,300, according to the state-run news agency. Dozens of others were reported dead in other towns in eastern Libya, he said.
Authorities have transferred hundreds of bodies to morgues in nearby towns. In the city of Tobruk, 169km east of Derna, the Medical Centre at the morgue in Tobruk received more than 300 bodies of people killed in the Derna flooding; among them were 84 Egyptians, according to a list of dead obtained by AP.
At least 10,000 people were still missing in the city, according to Tamer Ramadan, Libya envoy for the International Federation of Red Cross and Red Crescent Societies.
Countries and agencies pledge support following the disaster
The UN has announced $10 million in aid in response to the flooding, which will be disbursed from its Central Emergency Response Fund.
In addition, the UK announced on Wednesday an initial package of up to £1 million ($1.2 million) in assistance to meet the immediate needs of those most affected by the floods.
The UK is working with partners on the ground to provide shelter, health care and sanitation.
“The UK is committed to supporting Libya following these devastating floods,” Foreign Secretary James Cleverly said.
“The funding announced today will provide life-saving assistance to those most affected by the floods, including women and children and those who have been displaced from their homes.
“We will continue to co-ordinate closely with the UN and the Libyan authorities on what further support may be required.”
Britain's King Charles III sent a message of condolence on Wednesday evening to the chairman of the Libyan Presidential Council, Mohamed Al Menfi, saying: “My wife and I are so desperately saddened by the devastating impact and loss of life caused by Storm Daniel and the subsequent floods.
“We mourn with all those who have lost their loved ones, and continue to pray for everyone whose lives and livelihoods have been affected by the horrific floods.
“I admire greatly all those who are engaged tirelessly in the rescue efforts in such dire conditions, and praise their selfless bravery.
“I know that my government stands ready to support your needs.”
The UAE has sent two aid planes to Libya carrying 150 tonnes of food and medical supplies.
The EU on Wednesday activated its Civil Protection Mechanism to help Libya, with Germany, Romania and Finland offering tents, field beds and blankets, 80 generators and food as well as water tanks.
The bloc said it was releasing an initial €500,000 ($536,000) in humanitarian funding.
The US is sending emergency funds to relief organisations and co-ordinating with the Libyan authorities and the UN to provide additional support, President Joe Biden said.
France said it would send a field hospital.
Firefighters from several Spanish provinces have travelled to Libya. Some carried boxes with electrical equipment, including generators.
A representative for the Basque NGO Accion Norte said eight firefighters, four rescue dogs, a doctor and an interpreter were en route to Derna, together with a contingent from the Valencia-based NGO Bombers pel Mon.
“We are completely self-sufficient and are carrying specialised equipment for rescue from collapsed structures and water rescue,” he said.
Italy on Tuesday said a team including firefighters and civil protection officials was departing for Libya.
On Wednesday the country's Defence Ministry said two military jets would travel to Libya with more firefighters, logistical supplies and other equipment. The naval vessel San Giorgio has also been sent to bolster logistical support.
The ministry says it might also send a second boat to bring more materials and two helicopters for the search and rescue operations.
The Italian Red Cross sent aid including sanitary facilities, drinking water purifiers, generators and 1,500 body bags.
Egypt said it would send a Mistral helicopter carrier to serve as a field hospital and set up shelter tents for those who lost their homes, state TV reported.
Jordan sent an aid plane carrying relief supplies including tents, blankets and food.
Tunisia sent aid and a civil protection team specialised in search and rescue with four dogs, a medical crew, thermal monitoring devices and a drone to detect victims, in addition to a field hospital.
Kuwait sent an aid plane carrying 40 tonnes of medical and relief supplies in addition to food.
Algeria is sending eight aircraft carrying food, medical supplies, clothing and tents.