Speaking on Thursday, President Emmanuel Macron promised necessary punishment for those involved.
On Dec. 10, Lactalis - one of the world's top manufacturers of dairy products - ordered a recall of 625 batches or almost 7,000 tons of products after almost 30 infants fell sick.
Le Maire fired harsh criticism against Lactalis before the press conference, calling it a "failing company".
The admissions by Carrefour, Leclerc, Auchan and Systeme U deepened a salmonella health scare that began in early December when France's consumer protection agency ordered the halt to sales and a global recall of products from a factory in northwest France.
But on Thursday Lactalis spokesman Michel Nalet said the company had "worked in flawless collaboration with state agencies" since the start of the crisis in December.
France, seeking to limit reputational damage to its agri-business industry, threatened on Thursday to impose sanctions after the country's big supermarkets said recalled baby foods made by Lactalis had still found their way onto shop shelves.
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Late Wednesday, retailer Intermarche Chairman Thierry Cotillard said that his company would "definitively" stop selling any infant products from Lactalis's brand Milumel, blaming the dairy group for the mishandling of the products recall.
A Casino spokeswoman told AFP that it had sold 352 items that should have been removed from shelves as part of the recall. Three dozen children have fallen ill.
Last week, a report said that French food safety inspectors failed to detect salmonella contamination at the Lactalis facility three months before the company carried out the recall.
In a statement on Thursday, Carrefour said it had sold 434 products at risk of contamination since the December 21 recall, but that another 95,000 had been successfully removed from shelves.
Salmonella symptoms include diarrhoea, fever, vomiting and abdominal pain, and are extremely unsafe for infants. The illness, caused by intestinal bacteria from farm animals, is especially risky for the very young and elderly because it can cause severe dehydration.
The company took internal recall procedures which led to the removal and destruction of more than 36,000 products but said the 52 products had "escaped the vigilance" of its teams.