IOWA CITY, Iowa (AP) – A retired superintendent of Effigy Mounds National Monument is facing a federal investigation three years after making a startling disclosure: He had a box of long-missing ancient Native American remains in his garage.

The investigation is separate from a recent scandal involving another former superintendent who oversaw $3 million in illegal construction projects at the 2,526-acre site in northeastern Iowa’s wooded hills along the Mississippi River. But it has become another headache for the National Park Service, which operates the property that features 200 Native American burial and ceremonial mounds, some of which are shaped like animals.

The case started in 2011 when former superintendent Tom Munson acknowledged that he had a box filled with prehistoric bones in the garage of his Prairie du Chien, Wisconsin, home and returned them to the monument. Those artifacts, including fragments of jaws and leg bones between 1,000 and 2,000 years old, had been housed in the museum’s collection after they were found at the site in the 1950s. The revelation of their whereabouts outraged some representatives of the 12 tribes who are affiliated with the monument and consider the site sacred.

“It was kind of a stomach-turning anger and disappointment,” said Johnathan Buffalo, historic preservation director for the Sac & Fox tribe.

After the discovery, current Superintendent Jim Nepstad formed a review committee that included archaeologists and tribal officials to examine what happened. Buffalo, a committee member, said all the missing artifacts have since been recovered and are in the process of being returned to tribes for proper reburial.

The U.S. Attorney’s Office is now considering whether to pursue any charges following an investigation by a special agent with the National Park Service. The Archaeological Resources Protection Act carries potential civil or criminal sanctions for damaging archaeological resources.

The 74-year-old Munson, who was park superintendent from 1971 until his retirement in 1994, has hired prominent Iowa City defense lawyer Leon Spies, who confirmed an inquiry is underway by federal prosecutors based in Sioux City and Cedar Rapids.

“It’s sufficient to say that he’s cooperating with the investigation and trying to provide as much information as he can to help out,” Spies said. He called Munson “a valued and dedicated employee” whose work as superintendent won wide praise.

A spokesman for the U.S. Attorney’s Office in the Northern District of Iowa declined comment. Nepstad said he didn’t want to jeopardize the investigation by discussing the case, saying it is “at a very sensitive stage.”

Another former monument employee, Sharon Greener, said Munson directed her to pack up the bones in two large cardboard boxes when she was a temporary employee in 1990 and they put them in Munson’s personal vehicle, Greener’s attorney Bill Roemerman said. Greener was told the artifacts were being taken out of the museum collection under a process known as deaccession, but later learned the proper steps hadn’t been followed and the removal was inappropriate, Roemerman said.

The motivation for the removal isn’t clear, and Spies said it wasn’t an appropriate time to detail Munson’s actions. But in 1990, a federal law called the Native American Graves Protection and Repatriation Act was about to take effect, which required museums to return many ancient remains and burial objects to tribes. Archaeologists worried the law would harm their research abilities.

Buffalo said he believed that Munson, like some other officials across the country, simply didn’t want to return those objects to tribes.

“He thought he was protecting something. He didn’t see us as human beings,” he said. “He just saw a science project.”

Greener kept an inventory of the artifacts that were placed in the boxes and told future superintendents about what happened, Roemerman said. Munson denied having them over the years when asked but acknowledged he had the bones in April 2011 after Greener brought the issue to the attention of Nepstad, who had recently taken over as superintendent, Roemerman said.

Nepstad replaced Phyllis Ewing, who was blamed for violating laws meant to protect the site in building boardwalks and a maintenance shed during her tenure as superintendent. Ewing was reassigned in 2010 and fired in February, weeks before the National Park Service released its 700-page report on that case.

Greener, who worked as administrative assistant under Ewing, has left the agency under the terms of a confidential separation agreement, Roemerman said.