The National Archives allege the 78-year-old used a fountain pen to change the date on a pardon from April 14, 1864 to April 14,1865.
The change made it appear as if Lowry discovered a document that could have been Lincoln's final official act before he was assassinated that evening at Ford's Theatre.
Lowry said he is a man of honor and denies that he altered the historic document.
Lowry's purported discovery was hailed by historians when he came forward in 1998. At the time, a Civil War expert with the Archives said Lowry had made "a unique and substantial contribution to Lincoln research and to the study of the Civil War."
However, an archivist became troubled with the document, saying the '5' appeared to be darker than the rest of the document and was perhaps covering another number. That archivist, Thomas Plante, took his concerns to the Archives' Office of Inspector General, where an investigator shared Plante's suspicions.
Lowry is a retired psychiatrist and a historian who has written numerous books on the Civil War. He has since been banned by the Archives from its facilities.
The Associated Press contributed to this report.