“The two children were not stillborn,” Florence Galtier, prosecutor in the southern town of Avignon, told AFP, citing an autopsy.
Their deaths were “not natural in origin”, she added, after the discovery at the home of a 41-year-old woman arrested last Thursday in the southern village of Bedoin.
The woman was charged Friday on suspicion of murder of two minors.
It is not known if she is the mother of the victims, both girls.
The autopsy showed one of the babies had suffered a blow leaving “cranial and intracranial” bruising, believed to be the cause of death.
Galtier said it was not clear if the injuries were the result of violence or a fall, a lack of care or something else.
She added it had also not been established if the girls were twins — or even unrelated.
Police received a telephone tip off from a man whose identity and potential connection to the case are also unclear.
France has known similar cases over the years.
Last March, a woman in her 30s was placed under investigation after two frozen babies were found at her home.
In 2015, five bodies were found in a similar case which saw the mother handed an eight-year jail term.
Another case which went down in French legal annals was that of Veronique Courjault, given an eight-year sentence in 2009 for killing three of her newborn children.
The bodies of two were discovered in a freezer in the home she shared with her husband in South Korea.