The creatures were carried along flood-swollen rivers, say the authorities.
“There is now a hippopotamus in [my] house,” Benue state resident Wuese Jirake told the BBC. “I hope that when it is tired, it may leave my home.”
Hundreds of thousands of people have been displaced by the flooding.
Hundreds also died in the worst flooding in decades.
Vast tracts of farmland have been completely destroyed.
‘Hope it will leave’
Mr Jirake told the BBC he had returned to his home to find it occupied by the hippo.
“This morning I visited my house. It is still inundated with the flood waters above my waist. There is now a hippopotamus in the house,” he said.
He said he had reported the situation to the authorities.
“I hope that when it is tired, it may leave my home. If there is any other way of dealing with the problem, the authorities need to pursue that because it is beyond my abilities.”
Similar situations have been reported in the towns of Makurdi, Agatu, Logo and Adoka, says the BBC’s Is’haq Khalid.
Nigeria’s National Emergency Management Agency says it is working hand in hand with the Benue state government and other relevant agencies to ensure the flood victims return to their homes.
The co-ordinator of the agency in north-central Nigeria, Abdussalam Muhammad, told the BBC that it was not safe for people to go back to their houses because of the presence of the dangerous animals.
“Presently there are crocodiles and snakes as well as other dangerous animals brought in by the floodwaters that are living in those houses, so, if the people return, it will be harmful to them and they will put their lives at risk,” he said.
He said people should wait for instructions after the floodwaters have subsided.