Initial tests found Peekaboo meatballs were contaminated with the banned food additive borax, they said.
The factory had been operating for about two years, producing up to 800 kilogrammes of meatballs a day, before it was raided on Thursday.
It sold its Peekaboo meatballs at more than 40 wet markets in Bangkok, Pathum Thani, Nonthaburi and Samut Prakan, its owner, identified only as Samrit, told officials.
It had just sold 65kg of Peekaboo meatballs to an unnamed international school in Pathum Thani for student lunches, FDA officials said.
The school has been warned not to serve the meatballs to students, they said.
FDA officials, and police, were acting on a tip that the factory, located in Khlong Luang district, was not complying with food-safety production regulations.
The factory was also using excessive amounts of food preservatives and failing to conduct quality-control checks.
It was also mixing chicken with pork in meatballs it advertised as being 100% pork, officials said.
Samrit has been charged with failing to comply with food-safety manufacturing standards and false advertising, police said.
He will be charged with producing contaminated food if further tests confirm the initial tests finding borax in his Peekaboo meatballs, FDA officials said, adding that tests will be conducted for other chemicals.
They seized more than 30 bags of meatballs, 13kg of pork and chicken, packages of the preservative sodium benzoate, and three meatball-making machines with meatballs inside them.