The princess earlier referred to "fractious" internal discussions, one day after an FEI advisory group recommended reforms and tougher sanctions in the Middle East-dominated discipline of endurance racing which has been beset by doping cases, some involving her husband's stables.
"We don't march in lockstep and nor should we," Princess Haya said in her opening address on Thursday. "But we always pull together when it matters and it matters now."
The FEI said 100 of its 132 national federations requested changing the term-limit rule, which was one of Princess Haya's key promises on being elected as a modernizer in 2006.
Delegates from Belgium, Sudan, Taiwan and Jamaica also spoke in support of the princess remaining in office, which would allow her to retain her International Olympic Committee membership.
Princess Haya staked her first presidential term on cleaning up the sport after horses tested positive for doping at the 2004 Athens Olympics and 2008 Beijing Olympics, requiring some medalists to be disqualified.
That FEI doping and integrity review was led by former London Metropolitan chief John Stevens, whose investigations agency is currently heading an internal inquiry of Sheik Mohammed's extensive endurance and thoroughbred stables in Dubai and England.
In May, British authorities seized a shipment of unlicensed equine drugs, including steroids, in a Dubai government plane which landed at Stansted airport near London.
"We all want a well-run federation that serves its national federations and athletes and is financially strong but, most importantly, ethically strong," Princess Haya told FEI members.