LEXINGTON, Ky. - A veterinarian once hired to evaluate the Thoroughbred Retirement Foundation's herd of about 1,200 horses says the retirement group must reduce its herd if it is to continue its mission of retiring former racehorses. The Thoroughbred Retirement Foundation's largest benefactor, the late Paul Mellon's estate, paid Dr. Stacey Huntington to examine the retirement foundation's herd, with organization's agreement. But the retirement foundation stopped cooperating with Huntington after the New York Times reported preliminary information from her evaluations, quoting Huntington, and alleged that many of the horses in the foundation's care were neglected, even to the point of starvation. The foundation has denied that it has a widespread problem with neglect but acknowledges that it has had financial troubles as donations have shrunk and its horse population has grown. The charity's most recent federal filings show a $1.2 million deficit in 2009. In a four-page letter accompanying her veterinary evaluations, Huntington reported that 98 percent of the 857 horses she examined needed dental care, farrier work, deworming or vaccination. She did not use the words "emaciated" or "starving" in the letter but wrote that she considered 25 of the 857 horses as having body condition scores of less than three, 116 as having scores of 3.25 to 4, 239 as having scores of 4.25 to 5, 403 as having scores of 5.25 to 6, and 66 as having scores greater than 6. READ: Dr. Stacey Huntington's evaluation letter [PDF] The Henneke Body Scoring Condition System, a standard evaluation system used by many equine rescue operations and law enforcement agencies, a score of three is considered "thin," four is "moderately thin," five is "moderate (ideal weight)," six is "moderately fleshy," and scores above six range from "fleshy" to "extremely fat." "TRF states that it regards a BCS of 5-7 as being ideal," Huntington wrote. "If that is the case, then 380 horses in TRF's care have less than ideal body condition scores." Huntington added that the scores did not correlate with age and said of the herd's elderly horses, "Many of them are in very good shape even though they are in their 20s. Euthanasia based on anything less than quality-of-life issues is usually not appropriate for a rescue, so encouraging sponsors for them can offset the higher costs for their care." "Of particular concern are the animals with a BCS of less than 4," Huntington wrote. "Not only does it cost more to bring these horses up to ideal weight, they are also more prone to opportunistic diseases and parasitism." Huntington recommended that the Thoroughbred Retirement Foundation reduce its herd size, raise satellite farms' per diem payment to at least $4 a day, develop a list of three to four veterinarians for every farm who will agree to perform yearly physical exams at no cost and dental work and fecal exams at cost, and work with other rescue and retirement organizations that can help place horses in adoptive homes. "It cannot be over-emphasized that decreasing the herd size is paramount to having TRF continue as an organization," she wrote. "While many in the herd will not have second careers due to injuries from their racing, at least 372 horses were evaluated as possible re-training prospects." She also recommends that the Thoroughbred Retirement Foundation limit the number of horses at any given facility to 50 and improve mentoring and training for satellite farm caregivers. Huntington's report also recommended closing two farms, whose names were redacted from the copy the Mellon estate provided Daily Racing Form. Huntington noted both satellite facilities are being "monitored by veterinary oversight on a weekly or monthly basis" at the Mellon estate's cost and showed "strong or overwhelming evidence of inadequate management." Huntington singled out a Virginia adoption center where she said the retirement foundation was paying for barn space but the horses were not kept in those stalls, and she said 12 of 63 horses there were referred for "urgent veterinary work" after she found more than a third of the population with moderate to severe skin infections. But she generally praised the "very experienced, knowledgeable directors" at the charity's prison programs, in which inmates care for horses at prison-affiliated facilities while learning horse care skills. And she suggested them as possible locations to start retraining horses for possible adoption. Mellon estate executor Beverly Carter called Huntington's report "straightforward" and said, "We are behind Dr. Huntington 100 percent." The Thoroughbred Retirement Foundation's chairman, Tom Ludt, said Huntington sent the organization a box containing the 857 evaluation sheets, including photographs of each horse, as well as the four-page letter, and that a foundation staff member is reviewing the documents. He also noted that the retirement foundation is completing evaluations that remained to be done after organization decided not to cooperate with Huntington. The retirement foundation is using a group of other veterinarians contacted by its herd management committee. Huntington's report first was quoted in a New York Times article published online on Thursday night. "There have not been glaring issues, and this has been misleading," Ludt said of the most recent Times article. "There have been horses that have needed teeth floating and things like that, but I've yet to see anything or be told anything contrary to normal issues for older horses coming out of a winter." Ludt also questioned Huntington's objectivity, saying a line in her report said she had been hired to do the herd evaluations because of her "several years of experience in working with law enforcement as a professional advisor in cases of animal neglect and abuse." "We've had two flaws: paying [satellite farms] on time, which is a lack of funds, and doing a better job of record-keeping," Ludt said, adding that the retirement foundation has not always kept track of its horses' exact ages. "I'm not sure how she knew the ages." Ludt said The Thoroughbred Retirement Foundation is working with The Jockey Club to verify the ages of its horses as well as to improve general record-keeping.