The basin, shared by Cameroon, Chad, Nigeria and Niger, "is experiencing the highest rainfall in nearly 30 years", the agency said in a statement.
Roughly 400mm (almost 16 inches) of rainfall has been recorded, sparking flash flooding in villages and fields, it said.
The region has been in the grip of a security crisis since 2015, when Nigerian jihadists began launching cross-border raids.
Two administrative departments in Chad, Fouli and Kaya, have been declared war zones by the authorities.
"Between August 8 and 16, 11,764 people were displaced in Fouli, Kaya and Mamdi, one of the highest numbers ever recorded by the IOM in such a short period, the agency said.
"Among them, 36 per cent were displaced as a result of floods and 64 per cent due to the worsening of the security situation."
The agency, an intergovernmental organisation specialising in help for migrants, refugees and displaced people, said it had dispatched more than 2,500 shelters and 2,700 hygiene kits, sleeping mats, clothes and cooking equipment.
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