Metabolife and Michael Ellis were charged with six counts of making "fictitious and fraudulent representations" to the FDA and two counts of "corruptly endeavoring to influence, obstruct and impede proceedings" concerning the regulation of dietary supplements containing ephedra being carried out by the FDA.
Until the sale of ephedra was banned last year, Metabolife's reputation as one of the largest retailers of dietary supplements in the US was based largely on sales of its ephedra-based product Metabolife 356.
Metabolife and Ellis are charged with claiming that that the company had never received notice about consumers suffering serious adverse health effects after taking its product and that the company had a "claims-free history", in letters to the FDA in 1999.
"We will pursue to the full extent of the law those who would seek to mislead consumers by providing false information or impeding investigations of risky products," said acting FDA Commissioner Dr. Lester Crawford.
Metabolife said it no longer sells ephedra-based products and instead sells a range of non-ephedra dietary supplements that are safe and effective when taken as directed.
The defendants are expected back in court on 7 September.
The ban on ephedra was the first carried out by the FDA under powers declared in the 1994 Dietary Supplement Health and Education Act (DSHEA), proving that the much criticized regulation could be used to protect consumers.
Last month, a Crosby woman who suffered brain damage in a stroke after taking ephedra received a $7.4 million jury award. A Southeast Texas jury awarded Rhea McAllister $2.4 million for damage caused by Metabolife's supplement and $5 million in punitive damages.