TAMPA, Fla.—Researchers excavating unmarked graves at a notorious reform school in the Florida Panhandle said Tuesday that they have retrieved the remains of 55 bodies, nearly double the number originally believed to be buried there over many decades.

The exhumations mark a milestone in a painstaking effort to unravel the longtime mystery of what happened to scores of children who were sent to the former Arthur G. Dozier School for Boys in Marianna, Fla., and died. The institution for wayward youth, which the state opened in 1900 and closed in 2011, faced allegations throughout its history of brutal beatings, rapes and forced labor. Relatives of boys who died there, as well as former students who survived, have long believed some kids perished in suspicious circumstances.

Despite a string of state and federal investigations over the years, school officials repeatedly denied wrongdoing. Florida Attorney General Pam Bondi, who supported the excavation effort, said, "Hopefully, surviving family members are closer to the closure they deserve. It's such a tragedy that so many young boys lost their lives there."...