In the experiment, aimed at testing the then-new drug penicillin, inmates were infected by prostitutes and later treated with the antibiotic.
"The sexually transmitted disease inoculation study conducted from 1946-1948 in Guatemala was clearly unethical," Secretary of State Hillary Clinton and Health and Human Services Secretary Kathleen Sebelius said in a statement.
"Although these events occurred more than 64 years ago, we are outraged that such reprehensible research could have occurred under the guise of public health. We deeply regret that it happened, and we apologize to all the individuals who were affected by such abhorrent research practices," the statement said.
The experiment, which echoed the infamous 1960s Tuskegee study in which black American men were deliberately left untreated for syphilis, was revealed by Susan Reverby, professor of women's studies at Wellesley College in Massachusetts.
She found out about it this year while following up on a book about Tuskegee and, unusually for a researcher, informed the US government before she published her findings.
"In addition to the penitentiary, the studies took place in an insane asylum and an army barracks," Reverby said in a statement.
"In total, 696 men and women were exposed to the disease and then offered penicillin. The studies went on until 1948 and the records suggest that despite intentions not everyone was probably cured," she said.
Her findings, to be published in January in the Journal of Policy History, link the Tuskegee and Guatemala studies.
"In 1946-48, Dr. John C. Cutler, a Public Health Service physician who would later be part of the Syphilis Study in Alabama in the 1960s and continue to defend it two decades after it ended in the 1990s, was running a syphilis inoculation project in Guatemala, co-sponsored by the PHS, the National Institutes of Health, the Pan American Health Sanitary Bureau (now the Pan American Health Organization), and the Guatemalan government," she wrote.
"It was the early days of penicillin and the PHS was deeply interested in whether penicillin could be used to prevent, not just cure, early syphilis infection, whether better blood tests for the disease could be established, what dosages of penicillin actually cured infection, and to understand the process of reinfection after cures."
The full paper is available at http://www.wellesley.edu/WomenSt/Synopsis%20Reverby%20'Normal%20Exposure'.pdf.
Dr. Francis Collins, director of the US National Institutes of Health, said regulation prohibited such "risky and unethical" research today. He said the revelations could damage efforts to encourage people to take part in medical research today.
"I think the track record in past 20-30 years has been quite remarkable," Collins told reporters in a telephone briefing.
"But we all recognize that the Tuskegee study which involved this same Dr. Cutler did great damage to the trust ... particularly from the African-American community and for medical research." Arturo Valenzuela, Assistant US Secretary of State for Western Hemisphere Affairs, said it was not yet clear whether any compensation would be offered. It was also not clear whether any of the people who were experimented upon could be traced, but said an investigation had been launched.
Collins said there were no records of the study at NIH other than the title of the original grant.
Cutler retired as a professor at the University of Pittsburgh in 1985 and died in 2003.
