Washington (CNN) -- Potentially hundreds of American veterans and their family members who were laid to rest at Arlington National Cemetery were misidentified or mislocated, including some in an area that includes grave sites from the wars in Iraq and Afghanistan, according to a new Army investigation.
The investigation culminated in a change in leadership at the historic cemetery that has been home to U.S. veterans since 1864.
"I deeply apologize to the families of the honored fallen resting in that hallowed ground, who may now question the care afforded to their loved ones," Secretary of the Army John McHugh said.
McHugh launched the Army inspector general's investigation last fall after reports of cremated remains being buried in the wrong grave sites, according to Army officials. It was an expansion of an ongoing investigation into cemetery management issues launched by previous Secretary Peter Geren.
The investigation cited missing burial records, unmarked graves and burial urns put in a spillage pile, where dirt dug up for grave sites is left.
Investigators also said inaccurate burial maps are a "systemic problem," which did not allow them to visit all the graves in question.
Army investigators found a "lack of established policies and procedures, a failure to automate records, and long-term systemic problems," documents show.
After reviewing the investigation, McHugh made immediate changes but did not fire anyone. Instead, he ordered punishments to the cemetery's leadership. Longtime Superintendent John C. Metzler was reprimanded, and his deputy, Thurman Higginbotham, was temporarily removed pending further review.
The general in charge of the Army investigation, Lt. Gen. Steven Whitcomb, said that two of the 211 mismarked graves were those of troops buried in the section reserved for those killed in Iraq and Afghanistan. McHugh said those problems had been resolved.
The other 209 or so were scattered among three other sites at the cemetery during an unknown period of time, Whitcomb said.
"I don't know that there could be many more, but there could be more," he said.
With the cemetery holding more than 300,000 graves going back almost 150 years, the Army admits it can't guarantee that all will be accounted for.
McHugh would not identify the names of the remains affected by the mismanagement.
"While the inspector general's team found that [cemetery] employees performed their jobs with dedication and to a high professional standard, they also found them hampered by dysfunctional management, the lack of established policy and procedures and an overall unhealthy organizational climate," McHugh said. "That ends today."
Some 330,000 veterans and their family members are buried at the tree-covered and hilly Arlington, Virginia, site overlooking the nation's capital.
McHugh said during a Pentagon press briefing Thursday that Metzler, the 19-year superintendent, will receive a letter of reprimand to last three years in his permanent work file. Additionally, Metzler will receive reduced benefits for his poor management of the facility.
Before Thursday's announcement, Metzler had filed for retirement effective July 2. But McHugh will not let him serve out his full duties, according to his letter of reprimand. Metzler will be responsible for funeral operations until his retirement, and the cemetery's management duties will be given to an interim superintendent.
"Given your decision to retire, I have elected not to initiate more severe disciplinary action," McHugh said in the letter of reprimand.
McHugh also created a position to oversee operations at Arlington and will himself oversee the superintendent position. Metzler's final duties will include ensuring a smooth transition for the person coming into this new position.
While Metzler is blamed for poor management, deputy Higginbotham is being looked at for improper activities, including making false statements to Army investigators, creating a hostile work environment, having unauthorized access to employee e-mails and signing a false document, according to Pentagon officials close to the case.
According to a Pentagon official not authorized to speak publicly about the case, the Army will ensure that Higginbotham will not work at the cemetery.
The Army has created a call center to address family concerns regarding burial discrepancies at Arlington National Cemetery. The number is (703) 607- 8199 and will be open from 8 a.m. until 9 p.m. beginning Friday.