The two-week search involved dozens of FBI agents, along with anthropologists, archaeologists, cadaver-sniffing dogs and a demolition crew that took apart a barn.
Louis Fischetti, supervisory agent with the Detroit FBI, said the tip that led agents to the farm was the best federal authorities had received since 1976.
The agency planned to continue the investigation into Hoffa's 1975 disappearance.
"There are still prosecutable defendants who are living, and they know who they are," said Judy Chilen, assistant agent in charge of the Detroit FBI.
The farm was once owned by a Hoffa associate and was said to be a mob meeting place before the union boss' disappearance.
Chilen said that she believes Hoffa had been buried on the farm and that she had no evidence it had been moved. Fischetti added: "We really don't have any indication that it was or wasn't moved."
Hoffa vanished after he went to meet two organized crime figures. Investigators have long suspected he was killed by the mob to prevent him from reclaiming the presidency of the Teamsters after he got out of prison for corruption. But no trace of him has ever been found, and no one was ever charged.
The farm was just the latest spot to be torn up in search of clues to Hoffa's fate. In 2003, authorities excavated beneath a backyard pool a few hours north of Detroit. The following year, police ripped up floorboards in a Detroit home to test bloodstains. But the blood was not Hoffa's.
Over the years, some have theorized that Hoffa was buried at Giants Stadium in the New Jersey Meadowlands; ground up and thrown into a Florida swamp; or obliterated in a mob-owned fat-rendering plant.
The FBI began the excavation May 17, digging at Hidden Dreams Farm, 30 miles northwest of Detroit. The search started after a tip from Donovan Wells, an ailing federal inmate who once lived on the farm and was acquainted with its former owner, 92-year-old Hoffa associate Rolland McMaster, according to a government investigator.
McMaster's attorney Mayer Morganroth said he was not surprised that the search was wrapping up with the mystery unsolved.
"We never expected that anything was there," he said, adding that the FBI probably felt pressured to respond to the tip, lest it seem as if it were not trying to solve the case.
The FBI said the search was expected to cost less than $250,000. The government plans to pay for the barn to be rebuilt.
Hoffa's son, Teamsters President James P. Hoffa, had no comment, nor did Hoffa's daughter, Barbara Ann Crancer, a judge in St. Louis.
James Elsman — a lawyer who says Wells told him he saw a grave being dug at the farm in 1976 and heard comments about Hoffa being buried — said Tuesday that Wells is allowing him to share notes of those conversations with the FBI. He said he has a meeting scheduled with the FBI but would not say when.
While many veteran investigators and Hoffa experts were skeptical about the search, the little community of Milford Township seemed to relish the attention. A bakery sold cupcakes with a plastic green hand emerging from chocolate frosting meant to resemble dirt. Other businesses sold Hoffa-inspired T-shirts and put up signs with wisecracks such as "Caution FBI Crossing Ahead."
Hoffa was last seen on July 30, 1975. He was scheduled to have dinner at a restaurant about 20 miles from the farm. He was supposed to meet with a New Jersey Teamsters boss and a Detroit Mafia captain, both of whom are now dead.