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For thousands of years, the bones of the tiny prehistoric people were preserved in a limestone cave on Flores, an Indonesian island. When news of their discovery broke last October, the remains of the 1-m-tall Homo floresiensis, nicknamed "hobbits," jolted the scientific world into rethinking the course of human development. Whether or not these relics from seven individuals, discovered by a team of Australian and Indonesian scientists led by archaeologist Michael Morwood, marked a new species, experts knew they were extremely important - and, it goes without saying, extraordinarily fragile.

The discovery prompted immediate controversy; disbelievers quickly emerged. Among them was Professor Teuku Jacob, a senior Indonesian palaeontologist, who was not part of the discovery team. Jacob argued that the bones were merely those of a small human with an abnormally small head. Late last year, in breach of a memorandum of understanding between Australian and Indonesian discoverers, Jacob removed the bones to his own laboratory - a move many believed was aimed at proving his own theory. That act ignited a public feud. But last month, when the bones were returned, the row turned nasty.

To their horror, scientists found that some of the specimens had been severely damaged; a pelvis was broken (possibly as a result of being dropped); a mandible had been snapped and crudely repaired; and the highly important solitary skull appeared to have had pieces rubbed, scratched and broken off it. It's now alleged that the damage was most likely caused by someone making a cast with a special substance that is painted or sprayed on and hardens into a rubbery mold. Equally infuriating to scientists is the possibility that the supposed illicit casting may have altered the skull so no exact record of it can now be made. "It's simply outrageous," says Peter Brown, the palaeontologist attached to the Morwood team. "It's commercial and intellectual property, and it's a unique cultural relic."

Brown used computerized tomography (CT) scans and computer imagery to make the Morwood team's cast of the skull. He claims the crude cast-making method that damaged the skull is illegal. "It's a bit like some scholar went to the British Museum and stole the Rosetta Stone and made a copy of it, trashed the original in doing it - then had the only copy,'' he says. Jacob denies that any damage was done to the bones in his lab - or even that a cast has been made. "(The Australians) blame us for everything," he says. "They think they own the skulls and they own the cave and they think Indonesia is part of Australia. The Indonesian government has regulations about making and selling casts. So you cannot make them easily. You have to follow the rules and the government can intervene if you make something wrong.''

But Brown believes he has proof that a cast was, in fact made. There are witnesses to the process in Jacob's lab, he claims, and part of the returned skull is covered in "red gunk" consistent with casting. He says there could be several reasons for making an illegal cast. Copies could fetch up to $5,000 from museums abroad. Jacob "might just want this copy for his private collection," he says. "But he's gone to a hell of a lot of trouble for something he's claiming is not important."

Although no unauthorized copies of the cast have surfaced, Morwood has drafted a letter asserting that the intellectual property rights to the bones, including casts, belong to the Jakarta Center for Archaeology, whose scientists are on his team. Morwood is seeking a senior figure from the center to sign the protest letter. By March 11, he'd found no one prepared to do so. The center's director, Toni Djubianto, says such action would only make matters worse. "It might light a fire," he says. "It might blow up." Unlike the fragile bones, the dispute is unlikely to be laid to rest for very long.

Email Rory Callinan: rory_callinan@timeinc.com.au

• Rory Callinan
• A bitter fight has broken out over the handling - and alleged misuse — of an ancient "hobbit" skeleton