It said it supported the rule change allowing low levels of certain non-steroidal anti-inflammatory drugs (NSAIDs) in horses, describing it as a "step forward".
However, it urged the FEI to delay implementation, citing several reasons. They included concerns it may "impact team participation" at the 2010 World Equestrian Games in Kentucky if introduced prematurely and without a "carefully prepared education and communication programme".
"The list includes medications that would be allowed in FEI competitions and which are already permitted in USEF competitions," it said.
"These medications are not considered by the World Anti-Doping Agency to be performance-enhancing in human athletes and, because of this distinction, they are not prohibited.
"While it is the human athlete that is solely responsible in making the decision to use these non-performance enhancing medications, it is the responsibility of the FEI to protect and ensure the welfare of our equine partners.
"By placing restrictions on the use of the NSAIDs to include low level administrations and continuing a rigorous programme of veterinary examinations and inspections, the FEI is providing for equine welfare while still prohibiting the non-judicious use of these and other medications consistent with the Clean Sport initiative."
THE USEF said while it fully supportied the change, it believed that the implementation of the rule on January 1, 2010, may be problematic.
"The addition of certain NASIDs to the permitted medication list will be new to many national federations and an education and communication plan needs to be implemented before the rule takes effect.
"FEI laboratories need to adopt standard identical protocols for testing so as to assure a level playing field for all athletes throughout the world.
"The USEF is also concerned that the premature implementation of this new rule may impact team participation at the Alltech FEI World Equestrian Games in Kentucky in 2010.
"Without a carefully prepared education and communication programme, a premature implementation of this rule is risky and has high potential of causing a series of unintended consequences.
"The USEF believe the passage of the 'progressive list' is a step forward in a commitment to horse welfare. The General Assembly of the FEI has made its decision but, we strongly encourage the FEI to delay implementation until such time that the laboratory procedures are in place and a communication and education plan has been launched."