Many worshippers also sustained severe injuries in the stampede.
The bodies of the yet-to-be-identified woman, her daughter and others were deposited at the Mainland General Hospital mortuary.
A source said the pastor of the church was arrested but later granted bail on self-recognition after his statement had been obtained by the police at Ikotun.
The police said the church, is located at number 13/15 Ewenla Street, Pab Bus Stop, Ikotun and that the incident happened during its monthly crusade.
Residents said the church usually attracted a massive crowd of worshippers in the service hosted by Pastor Odekunle also known as Olorun Ojiji.
It was learnt that trouble started after the crowd, waiting for the second service, struggled to enter the venue immediately after the first service without allowing the first set of worshippers to exit the place.
This, they said, led to the stampede.
Lagos State Police Public Relations Officer, Benjamin Hundeyin, confirmed the incident.
“The victims include a woman of about 45-year-old and a 5-year-old girl, both name and address yet unknown. They gave up the ghosts. The scene has been visited by the police while the corpses have been deposited at Mainland General Hospital mortuary, Yaba, for preservation. Investigation is in progress and further development will be communicated,” he added