The report comes a day after President Umaru Yar'Adua insisted the military had won control of the area.
National Emergency Management Agency spokesman Apollus Jediel says about 1,000 people fled their homes in Maiduguri on Wednesday alone. His agency is urging state governments to send relief goods to help the displaced people.
Militants seeking to impose Islamic Shariah law throughout this multi-religious country attacked a police station in Bauchi state on Sunday. The violence quickly spread to three other states.
Scores of people have been killed in the violence. Police say most of the dead are militants.