In the experiment, aimed at testing the then-new drug penicillin, inmates were infected by prostitutes and later treated with the antibiotic.
"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.
Clinton called Guatemalan President Alvaro Colom on Thursday night to inform him, said Arturo Valenzuela, assistant secretary of state for Western Hemisphere affairs.
"They were obviously concerned about this information. They were saddened by it," Valenzuela said in a telephone news conference Friday.
Guatemalan officials took into account that the experiments occurred more than 60 years ago, Valenzuela said.
The study came to light recently when Wellesley College researcher Susan Reverby found the archived but unpublished notes from the project.
The scientific investigation, called the U.S. Public Health Service Sexually Transmitted Disease Inoculation Study of 1946-1948, aimed to gauge the effectiveness of penicillin to treat syphilis, gonorrhea and chancres.
Penicillin was a relatively new drug at the time.
A similar study was conducted between 1932 and 1972 in Tuskegee, Ala., on nearly 400 poor African-American men with syphilis whose disease was allowed to progress without treatment. The subjects were not told they were ill.
The Guatemala study was done under the direction of U.S. Public Health Service physician John C. Cutler, who later ran the Tuskagee experiment, said Dr. Francis Collins, director of the National Institutes for Health.
Collins, who called the Guatemala study "a dark chapter in the history of medicine," spoke at the same teleconference in which Valenzuela made his remarks. U.S. officials stressed Friday that ethical safeguards would prevent such abuses from occurring today.
"The study is a sad reminder that adequate human subject safeguards did not exist a half-century ago," the U.S. statement said. "Today, the regulations that govern U.S.-funded human medical research prohibit these kinds of appalling violations."
Clinton and Sebelius said the United States is launching an investigation and also convening a group of international experts to review and report on the most effective methods to make sure all human medical research worldwide meets rigorous ethical standards.