The International Organization for Migration mission in Libya said more than 5,000 people were presumed dead, with 3,922 deaths registered in hospitals, and over 38,640 were displaced in the flood-stricken region.
Tariq Kharaz, a spokesperson for the eastern authorities, said 3,200 bodies had been recovered, and 1,100 of them had yet to be identified.
The International Federation of Red Cross and Red Crescent Societies (IFRC) also said that the number of victims could reach thousands.
Mahmoud Hamza, head of the powerful 444 Brigade, was seized by the Special Deterrence Force on Monday as he tried to travel from Tripoli's Mitiga airport, which the SDF controls.
Saif al-Islam al-Gaddafi, 49, appeared in an electoral commission video for the first time in a decade.
In May, 108 migrants and refugees were sent to the Tajoura detention centre near Tripoli, which was hit by air strikes on Tuesday night, killing at least 53 people.
The health ministry said that apart from the attackers, three people had been killed and at least 21 injured.
BBC, quoting a report said that a 5 million children were at the risk of famine, disease and bombs.