Almost 2,000 human bones from ancient Native American burial sites have been discovered among tens of thousands of rare cultural artefacts by FBI art crime detectives at an Indiana home.

An FBI investigation determined that Don Miller, who died in 2015 aged 90, collected the objects in violation of several treaties and federal state statutes.

“To the best of our knowledge right now, those 2,000 bones represent about 500 human beings,” Tim Carpenter, who heads the FBI's art theft unit, told CBS News.

Mr Miller who died in 2015, aged 90, collected artefacts from around the world including pre-Columbian pottery, Ming Dynasty jade, an Egyptian sarcophagus and a dugout canoe that had travelled down the Amazon River.

Talking on Tuesday to CBS This Morning, Mr Carpenter said that, before his death, Mr Miller admitted that he had come by many of the items illegally. He said that he had gone on unsanctioned archaeological digs all over the country and the world.

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He also came to agree that the artefacts should be returned to their proper homes. But since he did not live long enough to see the investigation run its course, many aspects of his life and the artefacts he left behind are a mystery.

The crime of digging up long-dormant graves has been an ongoing source of frustration for Native-American communities.

Towards the end of the 19th century, amateur and professional archaeologists alike began running roughshod over tribal burial grounds, excavating the skeletons of indigenous people who had died hundreds of years before.

Some bone fragments were displayed in museums while others were closely analysed by anthropologists looking to test since-debunked theories of race science, such as the belief that intelligence was directly correlated with skull size.

It took nearly 100 years before the Native American Graves Protection and Repatriation Act was signed into law in 1990, making it illegal to buy or sell Native American remains.

“All too often here we have been treated as curiosities rather than a people,” Pete Coffey, a tribal official with North Dakota's Mandan, Hidatsa and Arikara Nation, told CBS.

“They could very well be my own great-great-great-great grandfather, or grandmother... I characterise it as being ripped out of the earth.”

Mr Coffey is one of the tribal leaders now working with the FBI to return the misappropriated remains to their original resting places, CBS reported.

Experts say they believe most of the bones that were found in Mr Miller's home were removed from burial sites in North Dakota, and that many belonged to the Arikara tribe. It's unclear whether Mr Miller had shown off the remains to people who visited his home, or whether he had dug them up himself or purchased them from someone else who did.

Until Tuesday, the FBI had remained circumspect about the 2014 raid, which did not result in Miller's arrest or any charges being brought against him. At the time, officials said that they had received tips about his cache of artefacts and were investigating to see whether any of the items were illegal for private citizens to possess.

In addition to Native American artefacts, Miller had reportedly collected priceless relics from countries including China, Russia, Peru, Haiti and Australia, and stored them in outbuildings scattered around his home.

Robert A Jones, the FBI special agent in charge of the case, told reporters at the time that Mr Miller's methods for procuring some of those objects had violated multiple laws and treaties, but also undercut that claim by acknowledging that the relevant statutes might not have been in place yet.

Mr Miller had started his collection eight decades before, when he first found arrowheads on his family's farm as a child.

Advocates for criminal justice reform and libertarian groups such as the Cato Institute were quick to criticise what they saw as an overly aggressive approach from the FBI, arguing that the government had offered no evidence that Mr Miller had done anything illegal.

Nearly five years later, the investigation is ongoing, and experts anticipate it could take decades to sort through the thousands of objects that the FBI seized, since determining their legality means first figuring out where and when each was purchased.

Some artefacts have already been repatriated. Bogota's City Paper reported last October that 40 pieces of pre-Columbian pottery, some dating to 1,500 BC, had been ceremonially returned by the US State Department after the FBI determined that Miller had smuggled them out of the country.

Other artefacts have been sent back to countries such as Canada, Ecuador, New Zealand and Spain, the FBI's Indianapolis bureau said in a tweet on Tuesday. An additional 361 items from Mr Miller's collection will be returned to China this week.

Speaking to the Star in 1998, Mr Miller said that he had been stationed in New Mexico during the Second World War and assigned to the top-secret Manhattan Project, where he claimed to have witnessed the detonation of the first atomic bomb.

When the war ended, he went on to spend 30 years working as an electrical engineer for the Naval Avionics Centre in Indianapolis, while simultaneously making trips to build churches in Haiti and Colombia.

After retiring at 60, he said he and wife Sue, a former high school teacher, regularly travelled to impoverished countries to do missionary work.

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All the while, he filled up their home with historical curios, including a Second World War-era Nazi helmet and a shrunken head whose provenance he did not fully explain.

A former co-worker told the Star in 2014 that Miller had used his ample vacation time at Naval Avionics to conduct amateur archaeological expeditions across the world.

They said that he often came back with wild tales about his misadventures, from winding up in a Mexican jail to being interrogated by Libyan soldiers who thought he had been sent by the CIA.

While those stories proved impossible to confirm, Mohr, his friend from church, recalled that Mr Miller had tried to leave Haiti with a few cannonballs, and ended up getting stopped at the airport at the end of their mission trip.

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In the months before his death, Mr Miller had retreated from public life, residents told the Star.

When a news crew from CBS showed up at the sprawling two-story house before Tuesday's broadcast, his wife said that she was unable to comment on the FBI's discoveries. A Chinese terra-cotta warrior statue was still standing outside the door.