The brand-name drug, Lariam, is manufactured by the Swiss company Hoffmann–La Roche.
Side effects for both Lariam and its generic equivalent include severe anxiety, paranoia, hallucinations and depression, according to the manufacturer.
The company has not manufactured the drug in the United States since 1998 when generic forms of mefloquine became available. But, according to Sullivan, Lariam is still available and "lingers on the market."
Company senior spokesman Chris Vancheri told ABCNews.com that generic mefloquine "distributed by other companies continues to be approved by the FDA as safe and effective medicines."
"The details in the adverse event report are unknown and, therefore, we cannot comment," he said.
But according to Time, last year forensic psychiatrist Dr. Remington Nevin testified in Congress on mefloquine's toxic effects that might mimic post-traumatic stress disorder and traumatic brain injury, as well as contribute to suicide and violence.
But infectious disease expert Sullivan said mefloquine is largely safe and that he, too, takes a weekly dose of it when traveling and has "never had any side effects."
But for those who do, they can experience vivid nightmares, sleep disturbances and difficulty concentrating. "Those are the top side effects and most of the published reports," he said.
The military has several drugs in its arsenal for prophylactic (preventive) treatment of malaria, a mosquito-borne disease that causes fever, chills and flu-like illness that, if left untreated, can cause death. An estimated 219 million cases of malaria occurred worldwide and 660,000 people died in 2010, most in Africa, according to the U.S. Centers for Disease Control and Prevention (CDC).
"The military uses a combination of drugs," Sullivan said. "It's a good drug, but not for people who have had seizures or brain disorders. Pertinent to the [Bales] case, those with traumatic brain injury are not recommended to take it."
Sullivan said the manufacturer also cautions against use of the drug by airline pilots and those who operate heavy machinery. "It's not that they can't, but it does have some side effects like dizziness that occurs in 5 to 10 percent of people taking it, and strange dreams," he said.
Typically, two other drugs are used as a "first line" by the military -- tetracycline and tetracycline, taken orally once a day, Sullivan said. But some soldiers are unable to take those drugs because of allergies or intolerance.
"Then they go to a couple of other second-line medicines that include mefloquine," he said. "But not for people with seizures or people with traumatic brain injury, that is part of the language on the label for the drug."
Bales was charged with 16 counts of premeditated murder, six counts of attempted murder and seven counts of assault. His only not guilty plea was to a charge of impeding the investigation by destroying a laptop computer. The judge accepted his guilty pleas and scheduled the sentencing for Aug. 19.
In a November preliminary hearing, several of his fellow soldiers testified that Bales returned to the base alone just before dawn, covered in blood, and that he made incriminating statements such as, "I thought I was doing the right thing."
Some of the blood on him was later matched to at least one of the shooting victims, according to prosecutors.
Evidence was also presented that suggested Bales carried out the massacre as revenge for previous attacks on his unit, particularly a roadside bomb attack a few weeks earlier that severely wounded a fellow soldier. Bales did not testify during the two-week hearing, which was to determine whether he would face a court-martial. But some of the surviving villagers did appear via satellite from Afghanistan.
Some of his squad mates acknowledged consuming alcohol prior to the attacks, but said Bales did not seem to have been incapacitated. At the June court hearing, the judge also asked Bales about his reported use of steroids to build muscle, which can increase irritability and anger.
As for the mefloquine, malaria specialist Sullivan said, "it was in the mix."
But he was hesitant to solely blame the drug on Bales' actions. "Whether it was synergistic or two plus two equals six or two plus two equals ten, without mefloquine, would the two other two factors have been avoided? It's hard to say," he said. "But they are a perfect storm and it did happen and he was on [mefloquine]."
He also would not go so far as to say that the drug could trigger violence.
"There have been reports," he said."But it's soldiers -- it's not like they are giving it to nuns. Honestly, we would have to see what Carmelite nuns would do [taking the drug.]"
ABC News' Christina Ng contributed to this story.