"We have what appears to be a long bone, maybe a femur, that is of sustantial size and appears to be cut off on one end," said Roderick Beverly, special agent-in-charge of the FBI's San Antonio division. "We also found what appears to be finger bones and parts of a hand.
"The bones appeared to be charred, like they were set on fire," Beverly said.
Burnt fabric was also found buried with the bones.
Investigators believe O'Hair, her son and granddaughter were killed, dismembered and dumped on the 5,000-acre south Texas ranch in 1995, although previous searches of the property failed to find any bodies.
Beverly would not comment on whether David Roland Waters participated in Saturday's search. Waters was to have gone on trial this week but he made an agreement with prosecutors Wednesday.
But a law enforcement source who spoke on condition of anonymity confirmed to The Associated Press that Waters was taken to the site Saturday. His two lawyers also were present.
About two dozen state and federal agents using three cadaver dogs began scouring a spot about 15-foot by 15-foot near a grove of live oak trees shortly after arriving at the ranch around 10:30 a.m.
Internal Revenue Service agents, Texas Rangers and local sheriff's deputies helped in the search.
The bones were revealed by agents using shovels and picks to dig about 2 1/2 feet down, Beverly said.
Beverly said the search would continue.
The agreement was ordered sealed by U.S. District Judge Sam Sparks, although media reports have said Waters, who faced kidnapping and extortion charges, agreed to lead investigators to the bodies.
The Associated Press objected to Sparks' decision to seal the agreement and a hearing is set for Monday.
Waters, 53, who worked as O'Hair's office manager, was convicted of stealing $54,000 in May 1995, before her disappearance, and placed on probation. He is now serving a total of 60 years for violating probation and for federal weapons violations.
O'Hair, 77 and suffering diabetes and heart disease when she disappeared, enjoyed calling herself the most hated woman in America. She was involved in successful court battles in the 1960s to ban prayer and Bible-reading in public schools.
O'Hair, son Jon Garth Murray and granddaughter Robin Murray O'Hair left their Austin home in August 1995. Breakfast dishes were still on the table and O'Hair's medication was left behind. The family's beloved dogs were left at the house.
They were later seen in San Antonio but dropped from sight along with about $500,000 worth of gold coins from one of O'Hair's atheist organizations.
Prosecutors contend they were dismembered at a public storage shed in Austin, placed in 55-gallon drums and dumped on the ranch property under Waters' directions.
O'Hair's disappearance wasn't reported for a year until her estranged son, William Murray, told Austin police she was missing.
Theories ranged from O'Hair having run off with money from her atheist organization, United Secularists of America, and that she went away to die somewhere where Christians wouldn't pray over her.