For years, almost no one at the Dozier School even knew about the burial ground in a clearing in the woods on the edge of campus. It was forbidden territory. The soil here, churned in places by tiny ants, holds more than the remains of little boys. Only now is it starting to give up its dark secrets: horror stories of state-sanctioned barbarism, including flogging, sexual assault and, possibly, murder.

That the Arthur G Dozier School – a borstal for delinquent boys founded in 1900 – was not a gentle place was well-established. Boys as young as six were chained to walls, lashings with a leather strap were frequent and, in the early decades, children endured enforced labour, making bricks and working printing presses. When it was closed in 2011, it had already been the subject of separate federal and state investigations.

But, as suspicions deepen about how the boys in the burial ground died, pressure is growing again on the state to shine new light into the darkest days of the school in Marianna, a Florida Panhandle town that once was a bastion of the KKK and the site of the 1934 lynching of Claude Neal. The pressure is coming from some of the school's survivors, from relatives of boys who died here, and from Florida's top US Senator, Bill Nelson.

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"Where there is smoke, there is fire," Senator Nelson declared last month, calling on the state to delay plans to sell off the 1,400 acres occupied by the old school so that a team of forensic anthropologists from the University of South Florida can complete a project begun last year to comb the campus for more graves. He wants any bodies found exhumed, identified and returned to the families they came from.

So far, the team, led by Erin Kimmerle, has focused its work around the once-secret cemetery. It knows that as many as 98 boys died at the school between 1914 and 1973. Since starting last year, Professor Kimmerle has found 19 previously undiscovered graves in addition to the 31 marked by steel-pipe crosses. That means 50 graves so far. Forty-eight have yet to be located, assuming graves were dug for each body.

"It's more than we anticipated," she says. "Our purpose is to explain who these children were, what happened to them and to understand what the story is that should be told." The official stance – that all the children died from accidents, such as fires and drownings, or natural causes – does not impress her. She cites the case of one child, Billy Jackson, whose cause of death was listed as kidney failure. There is a record of his being beaten two weeks earlier and admitted to hospital. "Common sense", she asserts, says he died from the beating.

The place of Dozier in Florida's history is already set and it's a shameful one. That is thanks in part to a group of Dozier survivors who call themselves the "White House Boys" because that was the colour of the small building where the floggings used to take place. A decade ago, they began finding one another by email and social networks and sharing their painful memories. In a book that Roger Dean Kiser eventually wrote about his time at the school – The White House Boys: an American Tragedy – he called it a "concentration camp for little boys".

Robert Straley, who has built a web site called whitehouseboys.com, was 13 when he was remanded there. Even now, he recalls the wardens with fear, including the one-armed Troy Tidwell, who, he says, beat him on his first day. "They were just totally out of control up there," he said. "The ones that got the most beating were the 11-year-olds. They liked to beat the little ones because they didn't have to be afraid of them coming back after them with a brick in the hands. The older the boys, the less beatings they got."

In the town of Marianna, conversations about the school are difficult. Calvin Creamer, 62, knew the school cobbler who made boots with markings in the heels so they could track the boys down if they ran away – and the leather straps for the floggings. "They were mean people to start with," he said of the men who dispensed the discipline. "Back then, it was torture for those boys. And the police didn't care either. They would strip them down and strap them to 50-gallon drums bear naked, and then they'd beat them."

Thomas McSwaine, 42, runs a pet adoption shelter in one of the old warden's cottages on the campus and has heard all the stories. About the worst is of one night when the wardens woke up some boys on the white side of campus – this was before desegregation – brought them to a field in the dark, gave them guns and told them to shoot anything that was moving. "When they flipped those lights on they saw all these black kids running across the field and they had to shoot them."

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John Trott, 70, was a student of juvenile justice in Florida when he went on a class visit to the school in 1965 or maybe the year after. "They took me to see a dormitory and the bunks were packed in so tight they were right up against each other. There were 50 or more kids and no one was awake watching them. I knew that wasn't right," he says, before adding, "I am sure there were sexual assaults, kids on kids, but as for staff on kids, I didn't see that."

Years later, working for the Florida Department of Juvenile Justice, Mr Trott found himself visiting Dozier annually. Now retired and living in Marianna, he spoke of what he knows. The more grave allegations he has trouble accepting. "I am not going to deny they used the strap. But the bodies and things … I don't buy the murder allegations. But I can't prove they didn't happen."

Professor Kimmerle plans to extend her search far beyond the little cemetery on Boot Hill into other areas of the campus. She is also seeking permission to begin the process of exhuming bodies and transferring them to a state medical examiner. If such stories as the one told by Mr McSwaine are true, and she finds evidence of boys having been shot, Dozier would instantly become a crime scene and Florida would be forced to open a much wider criminal investigation, which in turn could lead to prosecutions.

For now, though, she has the more modest goal of helping people such as Glen Varhadoe, whose uncle, Thomas, arrived at the school on 22 September 1934 and was dead before the end of October. A letter was sent to his mother two weeks later, too late for a funeral and too late for questions to be asked. The alleged cause of death: pneumonia and anaemia. "How could a child of 13 who was in perfect health go to a school in Marianna where the mean average temperature was about 29C and die of pneumonia in 35 days unless he was being mistreated somehow?" he asked last week.

No one has ever been able to say where exactly Thomas Varhadoe was laid to rest. Now, his nephew thinks there is some small chance that Professor Kimmerle and her team will find him at last. If they do, he will reclaim him. "That's my mission. I just want to bring him home." Away from Marianna.

'They had literally ripped the skin off from his lower back to below his butt. It was like hamburger meat'

Robert Straley was sent to the Dozier School in 1963 for running away from home. He was 13 years old and, as he tells The Independent on Sunday, he got into trouble straight away.

"I was 105lb then and I was already being pushed around a little in the dormitory. I went and sat with a group of boys and they were talking about running away. I was tired of running and I didn't think the place looked so bad. I said, 'No, I am going to stick it out here.' But someone behind heard us talking and snitched on us. At about eight o'clock, Troy Tidwell [a warden] took us down to the White House. They opened the door and they lined us up against the wall. They had turned on an industrial fan to make a big racket to smother the noise of the boys.

"I was at the end of the line. I had never heard anyone scream and cry out in real pain like that and it was shocking. When the boys came out, their heads were down and their hands were buried in their crotch; they had glazed eyes and they were walking kind of stiffly.

"When it was my turn, I was already in shock. It was like a dream. You can't believe it's happening.

"I walked in and there was this single cot with a stained mattress. They told me to lay down and not to let go of the bed rail. I did let go of the rail because I had to see what it was they were hitting me with. When I turned, two men were on me, they grabbed my arms and legs and I got 10 more lashes. But I could see what it was: it was maybe four inches wide and least one inch thick and double-sewn, and it had a metal sheet in between. It was as heavy as a baseball bat.

"If you ran away they would give you 100 lashes with this strap. I will never be able to forget this one boy. He was 15, I think – maybe a little bigger than me – and they had literally whipped the skin off from his lower back to below his butt. It was just like hamburger meat."