The department sent cease-and-desist letters in February to co-directors of the Hippocrates Health Institute, Brian Clement and his wife, Anna Maria Clement, saying it had "probable cause" to believe they were practising medicine without a license.
A department spokesman says the orders were withdrawn due to "lack of evidence."
In a statement, Clement says the decision is proof that he and his wife are licensed nutritionists who "have not and do not practice medicine."
Last year, two First Nations girls went to the spa after stopping chemotherapy treatment for leukemia in favour of traditional aboriginal medicine and other alternative therapies.
The families of both girls say they went to the spa to relax and eat better.
Makayla Sault, an 11-year-old member of the Mississaugas of the New Credit First Nation, located near Brantford, Ont., made headlines when she abandoned her cancer treatment to go to the Florida spa.
Her family blamed chemotherapy for the stroke that killed her in January, but oncologists said that untreated leukemia can in fact cause strokes.
In a second case from the Brantford area, a judge ruled an 11-year-old girl with cancer had a constitutional right to opt for traditional medicine over chemotherapy.