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...