Roderick Beverly, special agent in charge of the FBI's San Antonio office, stopped short of confirming the identity of the bodies, but he said officials believe the search is over.
Investigators believe O'Hair, her son Jon Garth Murray and the granddaughter she had adopted, Robin Murray O'Hair, were killed, dismembered and dumped on the private, 5-000 acre ranch in 1995.
O'Hair had a hip replacement operation several years before her disappearance.
"The bones indicate three sets of human remains," Beverly said. "All appeared to have their legs cut off. The remains and the ground around the bones were charred, indicating a fire at the scene.
"The likelihood of three individuals walking around here, one of which has a hip replacement, and the trauma and marks we see on the bones, it's a better than even chance" that the remains belong to the O'Hair family, he said.
Beverly said investigators also expect to find partial remains of Danny Fry, who was a suspect in the family's disappearance. His body was found in the Dallas area, but the head and hands had been severed.
David Glassman, a forensic anthropologist at Southwest Texas State University, will take the remains to the university for analysis. Autopsies could take a week to 10 days.
As law enforcement officers came and went through the ranch gate Sunday, a man walked down the road pulling an 8-foot wooden cross.
"I'm not doing it for her, I'm doing it for her family," said Bob Hanus, 35, a self-described Christian missionary. "I said, 'What better place to go and pray.'"
Investigators got their break in the O'Hair disappearance on the eve of the trial of David Roland Waters, who faced kidnapping and extortion charges in the case. Waters made an agreement with investigators Wednesday that was ordered sealed by a federal judge in Austin.
A law enforcement source who spoke to The Associated Press on condition of anonymity confirmed that Waters was taken to the ranch Saturday. His two lawyers also were present.
A hearing is scheduled Monday to hear objections from The Associated Press on the judge's decision to seal the agreement. Waters' attorneys had made the request.
O'Hair, Jon Garth Murray and Robin Murray O'Hair left their Austin home in August 1995 under mysterious circumstances. 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 in gold coins from one of O'Hair's atheist organizations.
Prosecutors contend the victims were dismembered at a public storage shed in Austin, placed in 55-gallon drums and dumped on the ranch property under Waters' directions. He worked as O'Hair's office manager before being convicted of stealing $54,000. He is serving 60 years in prison on weapons charges.
Last August, Sparks sentenced Gary Paul Karr, 52, a former jailmate of Waters, to life in prison for extorting money from the O'Hair family.
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. Others said she went away to die privately where Christians wouldn't pray over her.