The shocking problem of unmarked or mislabeled graves at Arlington National Cemetery is "not a concern" at the 131 national cemeteries that are not controlled by the U.S. Army, the Department of Veterans Affairs says.

An investigation by Sen. Claire McCaskill, D-Mo., chairwoman of an oversight panel on the Senate Homeland Security and Government Reform Committee, has revealed that between 4,900 and 6,600 graves may be unmarked or mislabeled on Arlington National Cemetery maps -- up to 31 times the 211 graves previously identified by Army investigators.

But the problem appears to be limited to Arlington and possibly the much smaller United States Soldiers' and Airmen's Home National Cemetery in Washington, D.C., which are the only two national cemeteries managed by the U.S. Army. Under the National Cemeteries Act of 1973, control of all other national cemeteries was transferred to the Department of Veterans Affairs, which now operates 131 national graveyards.

Michael Nacincik, spokesman for the Department of Veterans Affairs' National Cemetery Administration, said the VA-operated cemeteries are the final resting place for more than 3 million U.S. veterans and average roughly 1,000 burials per day. Last year alone, he said, more than 106,000 burial ceremonies took place at the cemeteries.

Nacincik said cemeteries controlled by the Department of Veterans Affairs began using a digitized in-house system in 1994 called Burial Operations Support System (BOSS) to manage operations.

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"It allows us to schedule the burial, to assign the burial location, to order the headstone and many other administrative functions automatically," he said.

At the time, the department spent $2.4 million to digitize roughly 2.5 million paper records. From 1999 to 2003, Arlington National Cemetery used a modified version of BOSS to schedule funerals, manage burials and order headstones, but in 2003, cemetery and Army officials moved forward with a plan to develop their own automated burial system known as Total Cemetery Management System (TCMS).

In 2005, Army and cemetery officials told Congress that they had jointly determined that BOSS could not accommodate the unique needs of Arlington National Cemetery. As a result, a contractor, Alpha Technology Group was later paid $5.7 million to digitize 330,000 burial records at Arlington National Cemetery.

And while the Department of Veterans Affairs has had instances of incorrect burials in the past, Nacincik said they are "very infrequent," citing the performance of the BOSS system.

"With the use of BOSS, it is very rare and it'd likely be human error that led to it," he said. "The accuracy of our burials and those records, for obvious reasons, are one of the most important things we do."

Referring to the errors that have been documented at Arlington, Nacincik said they are "not a concern for VA cemeteries."

Nacincik said his agency is prepared to assist Arlington officials in any capacity it can, including demonstrating how the BOSS system can accommodate the national cemetery's unique requirements.

"We have demonstrated BOSS to them and showed it to them," he said. "We're certainly willing to do anything we can to help them, whether that be through personnel, technology or training.  Everything is on the table."

John Metzler, who served as Arlington's superintendent for 19 years, said he accepts "full responsibility" for the problems and seemingly suggested to a Senate panel on Thursday that cemetery employees were to blame for the system used to track gravesites that primarily relied on a complicated paper trail.

"Personally, it is very painful for me that our team at Arlington did not perform all aspects of its mission to the high standard required," Metzler told the panel. "As you evaluate these issues, it is important to fully appreciate that the complexity and breadth of operations at Arlington National Cemetery are unique and extraordinary. This complexity and breadth only increase during my tenure."

Metzler and his deputy, Thurman Higginbotham, were forced to retire after Army investigators found 211 graves in three sections within the 146-year-old cemetery that were either misidentified or unmarked.

Kaitlin Horst, a spokeswoman for Arlington National Cemetery, said Metzler addressed why the cemetery did not utilize BOSS during Thursday's hearing, but could not provide Metzler's testimony. A staffer at McCaskill's office told FoxNews.com that cemetery officials indicated that they simply determined the system was "not compatible" for its needs.

Mike Picerno, director of Calverton National Cemetery in Calverton, N.Y., said at least 12 checks are performed to ensure that caskets are interred properly.

"We're not aware of any problems anywhere remotely resembling Arlington," he told FoxNews.com. "I feel very, very confident that we're doing the right thing."

Ryan Galucci, a spokesman for AMVETS, an organization representing more than 180,000 veterans, said his organization believes the grave mismanagement at Arlington does not extend to other national cemeteries.

"We're certainly following the situation," Galucci said. "But a mistake like this just can't happen. It's inexcusable. It's insulting to veterans and family members whose loved ones are buried at Arlington."