The police found at least two fresh human heads when they arrested 11 people from the restaurant including the owner, six women and four men, following a tip-off, said an IBT report.
The heads were found wrapped in cellophane sheets.
Officials have also seized two AK-47 rifles, other weapons, dozens of rounds of ammunitions and several mobile phones during the raid.
A pastor, who was shocked to know that what he had eaten was human meat, complained to the police.
"I went to the hotel early this year, after eating, I was told that a lump of meat was being sold at N700 (£2.5), I was surprised. So I did not know it was human meat that I ate at such expensive price," the unidentified pastor said.
Reports of cannibalism sometimes emerge in Nigeria, but this is the first time a restaurant has been booked for selling human meat dishes.