A senior State Department official tells ABC News that under rules in place while Clinton was secretary of state, employees could only use private email accounts for official business if they turned those emails over to be entered into government computers. They were also forbidden from including sensitive but unclassified information on private email, except under some very narrow exceptions.
This policy is still in place, according to the Department. Until any private emails are entered into government computers, the official says, an employee is in violation of the rules.
Clinton used a private email account for her entire tenure as secretary -- and did not even have a government-issued email. She only turned over some 55,000 pages of emails to be entered into government computer systems late last year, nearly two years after she stepped down from the State Department.
It is also likely that some of Mrs. Clinton's emails contained information "sensitive but unclassified" as defined by the federal government, a senior State Department official acknowledged, in potential violation of the 2005 department regulation as codified in the Foreign Affairs Manual (FAM).
"Reports claiming that by using personal email [Clinton] is automatically out of step of that FAM are inaccurate," the official told ABC News in a statement. "We are not going to prejudge the outcome of the review of Secretary Clinton's 55000 pages of emails."
A spokesman for Clinton did not respond to ABC News' repeated requests for comment.
If Clinton has now turned over all emails related to official business, she would be in compliance with State Department rules, an official said. But there is no way to independently verify that she has done that.
Clinton’s spokesman said earlier this week that she has turned over about 90 percent of the emails she wrote as secretary of state, withholding only those that were strictly personal and not covered by the policy.
State Department email rules became an issue while Clinton was secretary of state.
One of Clinton’s ambassadors was criticized by the department’s inspector general in a 2012 report for using private email.
“It is the department’s general policy that normal day-to-day operations be conducted on an authorized information system, which has the proper level of security controls,” the Office of Inspector General wrote in the 2012 report, referencing the Foreign Affairs Manual provision dating to 2005.
The IG report warned that the use of non-governmental email accounts “increases the risk” of security breaches and the “loss of official public records as these systems do not have approved record preservation or backup functions.”
Clinton is believed to have established her own private email network based out of her Chappaqua, New York, home, where aides say she has personally preserved all messages before turning them over.
Clinton tweeted late Wednesday that she has asked the State Department to publicly release all the emails she turned over, but she has otherwise remained silent on the controversy.
Back when she last ran for president, Clinton was vocal about other government officials who use private emails that circumvent automatic government archiving.
“Is that what we really want in a presidential candidate and is that really what we want in a president?” former South Carolina Democratic Chairman Dick Harpootlian said in an interview with Jake Tapper on CNN.
ABC News' Shushannah Walshe, Liz Kreutz and Devin Dwyer contributed to this report. This story has been updated to include comment from the State Department.