The company doing the work recommended treating the site like a graveyard until more testing can be done, the Times reported.
“This randomness might be expected in a clandestine or informal cemetery, where graves were excavated haphazardly and left unmarked,” the company said in its report.
The state said there were 31 burials at the school in 2009. University of South Florida researchers later found an additional 24 graves.
An estimated 100 boys died at the school between 1900 and 1973. It was permanently closed in 2011.
The school is on about 1,400 acres near Marianna, about 60 miles from Tallahassee.
The Associated Press contributed to this report.