In separate flooding in the southeastern state of Cross Rivers, about 49 coastal communities are threatened, the Nigerian newspaper Leadership reported.
In Jigawa, more than 2,000 flood victims were being housed at a secondary school in Ringim, said Musa Illalah, a zone coordinator for the National Emergency Management Agency.
More than 16 villages in the area were "under serious threat" from the floods, said local government chairman Murtala Abubakar.
In Cross Rivers, which touches the Atlantic Ocean, rising waters in the Lagdo dam in neighboring Cameroon has swollen rivers, submerging farmlands, said Vincent Aquah, director-general of the state's emergency management agency.
Hundreds of homes have been flooded and more than 10,000 livestock affected.
He feared that the unprecedented level of flooding would cause extreme famine from the loss of crops and create housing problems for families who needed to be relocated.
In the north, Illalah said NEMA was preparing strategies to prevent the yearly flooding and reduce the threats throughout the region. He said two refugee camps had already been established.