It has been embraced by some of the biggest forces in the sport: the Jockey Club has given the foundation nearly $250,000 over the past two years, and individual owners — like Mike Repole, the co-founder of Glaceau water and the owner of the current Kentucky Derby favorite, Uncle Mo — have given sizable contributions as well.

Over the years, the foundation’s board has included some of the sport’s most influential owners, and the farms it contracts with have been homes to many of the horses those owners have bred and campaigned. Beam Us Up, an accomplished racehorse bred by Richard Santulli, the former chief executive of NetJets, was recently removed from one of the contract farms because of neglect. Santulli’s wife, Peggy, is on the T.R.F. board.

The findings of the veterinarian hired by the Mellon estate, Dr. Huntington, moved the estate’s trustees to send the farms money for things as basic as food. She found that some 25 percent of the horses have required some kind of urgent care, which the Mellon estate has provided, costing it “tens of thousands” of dollars, said Ted Terry, one of its trustees.

Dr. Huntington found that the foundation’s education of the caretakers and oversight of their farms had been poor. At one farm, Dr. Huntington said, the horses were being fed cattle feed that contained a toxic element.

“The horses are getting the short end of the stick from this group that advertises itself as advocates of horses,” Dr. Huntington said.

The most dramatic instance of neglect discovered so far, she said, was at the 4-H Farm in Okmulgee, Okla., where the owners, Alan and Janice Hudgins, would not let Dr. Huntington onto their property to inspect T.R.F. horses until the foundation gave them $20,000, a partial payment of what was owed them for taking care of 63 horses since 2005. They also forced the foundation to sign a pledge not to prosecute them for the condition of the horses.

When the horses were released, the 47 survivors were in such poor condition that Dr. Huntington filed a report with the Okmulgee County sheriff’s office. Her report included photographs of the malnourished horses, three of them considered starving. Nearly all of them needed urgent care.