The governing body said on Wednesday it sent allegations against the UAE equestrian body to its integrity unit, run by former London Metropolitan Police chief John Stevens.
The claims by British newspaper The Telegraph follow widespread reports of doping and horse abuse in endurance racing in the Middle East. The discipline is popular in the region with royal family members often competing in races of up to 120 kilometres (75 miles) across the desert.
Last month, the FEI withdrew recognition for the two remaining UAE-hosted endurance events, in Abu Dhabi and Dubai, on the international race calendar.
The UAE federation has allegedly registered results with the FEI for "ghost races." The Telegraph reported that results — with detailed interim times and speeds — appeared to be copied exactly from earlier valid races.
Faking results could put the welfare of horses at risk by clearing them to compete at a higher level beyond their ability or fitness levels.
If the allegations are proven, the UAE could forfeit hosting the endurance world championships scheduled in Dubai in December 2016.
The FEI acted against the UAE last month after an international furor, when images circulated of a horse with two broken forelegs dying at a national-level race in January in Abu Dhabi.
The UAE federation did not immediately respond to calls and emailed requests for comment.