A 47-year-old woman died from her injuries on Tuesday morning after the accident.
A six-year-old girl died on Sunday shortly after part of the floor collapsed.
A group of around 100 people were worshipping on the first floor of the building in Stains, in the northern Paris suburbs. Most were from the city's Haitian community.
At around 1.30pm on Sunday afternoon around 30 square metres of the floor collapsed.
Worshippers fell around 2.5 metres (7.5 feet) and 32 people were injured. A third girl of two-years-old was still in a critical condition on Tuesday.
The pastor and the owner of the building were both taken in for questioning by police on Tuesday evening over the deaths.
Le Figaro newspaper reported the two were being questioned over "involuntary homicide and aggravated injury."
The newspaper reported they had violated a "safety obligation" that applied to the building.
There have been suggestions that the building was not suited to a gathering of Sunday's size or nature.
Le Figaro also reported a police source who claimed things were "very festive. People were praying, chanting and dancing."
The town's mayor has said that work carried out on the building several years ago was done without authorisation.
"The local authority noted in 2008 that an extension was built without the right authorisation," said Michel Beaumale.