The horses were due to be euthanized because they were infected with the protozoal parasite that causes the disease.
They were removed under cover of darkness and have not been seen since.
Dr John Clifford, deputy administrator for the Animal and Plant Health Inspection Service of US Department of Agriculture, revealed that needle-sharing was behind the spread of the disease.
Its latest report to the World Organisation for Animal Health, dated September 15, reported that the outbreak had been resolved.
The first case was reported in June and appropriate quarantines put in place. Subsequent testing revealed seven horses in Missouri were positive for the disease, which can be spread by ticks or needle sharing.
"All evidence indicates that ticks did not play a role in the epidemiology of this event," Clifford reported, saying four ticks found and tested were not species known to transmit the organism.
"Transmission of the disease was associated with poor management practices that resulted in the transfer of whole blood between horses (needle sharing)," he said.
"All positive equine piroplasmosis horses were infected in the same manner. Five horses testing positive for equine piroplasmosis were destroyed.
"All other equidae on the index premises and in all epidemiological traced premises tested negative for equine piroplasmosis."
Clifford said the investigation into the illegal removal of the horses from the index premises continues to be conducted by law enforcement agencies.
"Non-substantiated accounts indicate that the illegally removed horses have been illegally transported out of country.
"All epidemiological investigations of this event have been concluded and, unless new law enforcement information is uncovered, this equine piroplasmosis event is considered closed."
A third horse in Kansas, which had earlier been with the Missouri animals, also tested positive for the disease. It also disappeared from quarantine, and efforts to locate it have been unsuccessful.