U.S. Attorney Kenneth Gonzales described the conduct alleged in the indictment as outrageous.
"No one should have to endure this type of experience simply because she or he accepts a food sample while shopping for groceries," Gonzales said.
Garcia, in shackles, did not enter a plea to the two counts. His public defender, John Van Butcher, was not available for comment after business hours Thursday.
The judge ordered Garcia to remain in custody pending a detention hearing Friday.
Garcia is accused in the three-page indictment of handing out tainted yogurt samples at a Sunflower Market in Albuquerque in January.
Officers responded to the store after a woman called to report an employee had given her what she was told was a yogurt sample. The woman told police she believed it was actually a bodily fluid.
Gonzales said his office will vigorously pursue anyone who deliberately taints food for the purpose of harming innocent customers, for malicious pranks or for deviant sexual gratification.
FDA investigators interviewed Garcia in March. The indictment said he falsely claimed not to know that the spoon he handed the customer contained semen.
Police said they tested the yogurt and found semen then linked it to Garcia using DNA.
Garcia was arrested Wednesday by Albuquerque police and officials with the U.S. Food and Drug Administration.
Chris Sherrell, Sunflower Farmers Markets president and chief executive, said in a statement the company "abhors the act that Garcia is alleged to have committed" and welcomed the federal indictment.
The company said it has cooperated fully with the FDA as well as state and local authorities since the incident was first reported in January. Garcia was fired by the company on Jan. 25.
Sunflower said it has no reason to believe the FDA or federal prosecutors intend to pursue any action against the company with regard to the yogurt incident. Spokesman Lew Phelps said the company "views this as a rogue employee who acted alone."