It was the second so-called baby-factory uncovered in a week in the west African nation.
"We acted on intelligence information and raided the house in Enugu (city) where we met six girls, under 17 and all pregnant, and freed them," police spokesman Ebere Amaraizu in southeastern Enugu state told AFP .
He said two men and a woman believed to be operating a child trafficking ring were arrested during the raid on Monday and were cooperating with police.
"Investigation will unravel the details. We have to know how they came about the pregnancy and where they came from," he said.
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Monday's raid came five days after police in nearby Imo State freed 17 pregnant girls and 11 small children from a home in the town of Umuaka.
The girls, aged between 14 and 17, told police that they had been impregnated by a 23-year-old man who is currently in custody. The owner of the building is on the run.
Human trafficking, including the selling of children, is the third most common crime in Nigeria behind fraud and drug trafficking, the United Nations cultural organisation (UNESCO) has said.