Monday's study does not prove that having any of these viruses causes harm, stressed co-author Dr. Harvey Alter of the National Institutes of Health.
But it strengthens suspicions, and the government has additional research under way to determine if the link is real or not.
Meanwhile, a group of French and Canadian scientists said it's time to test whether antiviral medications like those used against HIV might treat at least some people with chronic fatigue.
The virus connection first made headlines last fall when Nevada researchers reported finding a specific type, named XMRV, in the blood of two-thirds of the 101 chronic fatigue patients they tested. But several other studies, including one from the Centers for Disease Control and Prevention, failed to find XMRV virus in patients, making researchers wonder if this was a false alarm.
Monday's study, published in Proceedings of the National Academy of Sciences, thickens the plot. This time, NIH and Food and Drug Administration scientists examined the blood of 37 chronic fatigue patients and again didn't find XMRV - but instead they found a group of closely related bugs named MLV-related viruses in 86 percent of the cases.
Testing of 44 healthy blood donors, in contrast, found evidence of those viruses in nearly 7 percent.
Various viruses have been linked to chronic fatigue over the years only to fall by the wayside as potential culprits in the mysterious illness thought to afflict about 1 million Americans. It's characterized by at least six months of severe fatigue, impaired memory and other symptoms, but there's no test for it and no specific treatment.
These MLV, or "murine leukemia-related viruses," are known to cause some cancers in mice, and the XMRV relative has been found in some human prostate tumors, too.
But there's no easy way to test for it, meaning studies of a link at this point must be in research labs, not doctors' offices, FDA and NIH researchers said Monday.
No one knows how people become infected, but Alter said a major study is under way to see if there's any evidence of transmission through blood.
In the meantime, federal regulations require that blood donors be in good health, said FDA's Dr. Hira Nakhasi.