That email is a message complimenting Clinton on her January 2013 testimony before a congressional committee, according to government lawyers.
Late last month, State Department lawyers disclosed there were potentially as many as 30 emails related to the 2012 attacks in Benghazi, Libya -- which killed four Americans, including U.S. Ambassador to Libya Christopher Stevens –- turned over by the FBI that had not been publicly released.
This set off a fresh wave of Republican criticism that the Democratic presidential nominee was not being forthcoming and making public all work-related emails she sent or received while serving as secretary of state during the Obama administration.
On Wednesday, department lawyers said a closer review showed most of those 30 messages have already been made public, a revelation Clinton supporters are sure to highlight.
"After completing its review of the set of documents previously identified as potentially responsive, State has determined that there is one responsive document that is not a duplicate of the documents provided by former Secretary Clinton in December 2014 and that had not been previously provided to Judicial Watch in this case," State Department Deputy Spokesperson Mark Toner said in a statement to ABC News.
"The email does not change the facts that have previously been made clear about the Benghazi attacks," he said.
The update on the emails came in a filing made Wednesday in a federal court, regarding lawsuits filed by the conservative legal group Judicial Watch. The group is seeking access to records related to Clinton’s time at the State Department.
The Justice Department closed its investigation into Clinton’s use of a private email server without filing any criminal charges, but the issue is being kept alive, in part, by Judicial Watch’s lawsuits and congressional Republicans who are pushing for further investigations.
It's unclear why the message from Shannon, now undersecretary of state for political affairs, wasn't produced in previous searches or among the roughly 30,000 emails Clinton's lawyers deemed work-related and turned over to the State Department two years ago.
Two other emails found by the FBI were "near duplicates" of previously-produced messages, Department of State lawyers said in the filing. Some of the messages contain what the department called "internal technical metadata" that the FBI captured or added as it retrieved the messages.
Judicial Watch is suing for the Benghazi-related records and said it rejects the State Department's description of the records as "near duplicates" and is still after all 30 messages turned over by the FBI.