The skeletons of 50 people remain boxed up in a sea container in the northern WA town of Fitzroy Crossing, after the excavation of an eroding cemetery that had bones poking from the dirt.

For years, the Fitzroy River was left to eat away at the old burial site, despite local Aboriginal people raising concerns about why the mainly 'white' town cemetery had been relocated, while the unmarked graves of their relatives were left to wash away.

Dozens of bones have been stored in a shipping container at Fitzroy Crossing. ( ABC Kimberley: Erin Parke )

A three-month excavation funded by the State Government has now wrapped up, with the Kimberley Aboriginal Law and Culture Centre saying six sets of remains had been identified.

"The whole process went well, with the elders involved and the local rangers working with the archaeologists," repatriations officer Neil Carter said.

"There were six remains that were identified … two had names on the body bags, two had hospital bands with their names on them, and two had dog tags with their names on it.

"There was also another man that the old people know who it is, because he was found with a whisky bottle … the old people who were present when he was buried remember he was buried with the whisky bottle."

Indigenous elders performing a smoking ceremony at the Fitzroy River cemetery. ( ABC Kimberley: Matthew Bamford )

Also among the graves dug up were the remains of a young girl whose parents were missionaries in the area in the 1980s.

They got in contact with the Kimberley Aboriginal Law and Culture Centre after the ABC reported on the dig getting underway.

The bones remain boxed up in small wooden coffins that were handmade at the local Men's Shed.

But the big wet season and uncertainty around funding means they are sitting, waiting for reburial, in an unmarked shipping container.

The State Government said there was money remaining in the original excavation contract to cover the reburial, but the Kimberley Aboriginal Law and Culture Centre was seeking extra funding to assemble elders from across the region to commemorate the repatriation.

"I will not feel satisfied until we have finally reburied the remains up at the new cemetery, and have a proper burial ceremony," Mr Carter said.

"Those people who were buried down there came from all over the Kimberley, because many were brought here in the missionary days.

"So we want to have a large ceremony inviting relatives of those people to commemorate that those remains have been saved from being washed away."

A photograph documenting remains exposed by erosion in Fitzroy Crossing. ( Supplied: Kimberley Aboriginal Law and Culture Centre )

Too little, too late

There is residual sadness and anger over why an intervention was not made earlier.

A digger searches for human remains outside the Pioneer Cemetery. ( Supplied: Kimberley Aboriginal Law and Culture Centre )

It is thought as many as 20 sets of human remains were washed away in the years before the WA Government agreed to the $700,000 relocation project.

Mr Carter, who lives in Fitzroy Crossing and oversees the return of stolen Aboriginal remains from museums around the world, doubts the situation would have occurred in an Australian city.

"I think the situation here in Fitzroy Crossing — how the river has been washing the bank away and having body bags hanging out from the bank — if that happened anywhere else, something would have been done quicker," he said.

"Because we think unfortunately there have been some remains washed away down river and lost — the official list [for the gravesite] shows 84 bodies and we have exhumed 50."

Local Aboriginal people speak with resignation about the double standards that have haunted their lives.

In this case, that the 'white' cemetery was relocated to a safe, dry location in 2001, but the mainly Aboriginal burial ground adjacent was abandoned on the eroding riverbank.

Kids find human skull while playing

Robyn Wilson's son found a skull while playing around the riverbank in Fitzroy Crossing. ( ABC Kimberley: Erin Parke )

Over the years, shocking discoveries were made, with resident Robyn Wilson's son finding a human skull in the riverbank in 2011 as he played with friends.

"My son and his friends were floating down the river, which is what they do every year when it comes flood time," she said.

"They went across to an island in the middle of the river and they saw what they thought was a turtle shell, but when they kicked it over they realised it was a human skull, so they brought it back to town and took it to the local police station.

"A couple of the boys said they had nightmares that night … and some of them felt a bit weird the next day."

The reburial is pencilled in for April or May, after the wet season rains have stopped.

It is expected most of the remains will be reburied at the new cemetery and the remainder will be handed over to the families from more remote areas, to return to the traditional country from which the people originated.