Flores, Minnesota's Kennys Vargas and free agent pitcher Emanuel Ramirez all received 50-game suspensions, and Astros pitcher Euris Quezada was suspended for 25 games.
Flores, Chicago's seventh-round pick in 2008, received a 50-game ban after testing positive for Methylhexaneamine. The substance, originally created as a nasal decongestant, has been found in dietary supplements under various names in recent years.
The Del Rio, Texas native was hitting .275 with seven homers and 20 RBIs in 40 games with the Smokies this year. He last played Aug. 9, going hitless to extend a 5-for-29 slump.
Vargas, a first-baseman with Rookie-level Elizabethon, tested positive for Phentermine, an appetite suppressant used for weight loss. The 2010 Gulf Coast League All-Star, who turned 20 last week, was hitting .322 with six homers and 33 RBIs in 44 games for the E-Twins.
Quezada received a 25-game suspension, although the Commissioner's Office did not specify what the violation was. Signed by the Houston Astros as a non-drafted free agent in 2008, Quezada was 1-3 with a 6.95 ERA in nine starts for Tri-City in his third Minor League season.
All three players will begin serving their suspensions immediately.
Ramirez, a 6-foot-4 right-hander who appeared in four games with Tampa Bay's Dominican Summer League affiliate, received a 50-game suspension after testing positive for metabolites of Stanozolol, an anabolic steroid linked to body builders and several former Major Leaguers. The suspension of Ramirez will be effective immediately upon his signing with another Major League organization.
Major League Baseball has suspended 45 Minor Leaguers in 2011.