Five horses at the Jackson County, Missouri, stable had already been euthanized because they had the blood-borne disease. It is believed the two other horses, which had also tested positive, were taken to avoid the same fate.
Equine piroplasmosis is transmitted to horses only by ticks and contaminated needles. Humans are at no risk of being affected by this disease.
The Missouri Department of Agriculture, in confirming the two horses were missing, said it had notified state officials and the Federal Bureau of Investigation. Locks to the building and stalls were cut to remove the horses.
Agriculture Department director Jon Hagler said: "We continue to do everything we can to locate the two piroplasmosis-positive horses.
"Although this disease is not easily transmittable and does not affect humans, it is a disease that, through ticks and contaminated needles, can have a great impact on our horse industry.
"The Department of Agriculture is working with local, county, state and federal officials to do everything we can to find these horses. We are asking anyone that has seen anything suspicious to notify their local authorities."
On June 4, agriculture officials were notified of a piroplasmosis-positive horse and immediately quarantined the Raytown Equine Centre and put all horses at the facility under 24-hour surveillance.
The quarantine, enacted by the Missouri state veterinarian, was put in place to prevent movement of any horses from the centre.
The missing horses, which are microchipped, went missing on Wednesday night.
Agriculture officials confirmed that five of the seven horses that tested positive for the disease had been euthanized with the owners' consent.
An infected horse will show symptoms in mild forms such as weakness and lack of appetite. More acute cases include fever, anemia, jaundice, a swollen abdomen and laboured breathing.
Horses that survive the acute phase of infection may continue to carry the parasites for long periods of time. There is no cure.