A report released Wednesday by the State Department’s internal watchdog raises questions about former Secretary of State Hillary Clinton’s claim that a large proportion of her emails were formally archived because they involved State employees using official email.

The State Department Inspector General review highlights that State staffers using an email system known as SMART did not have their emails automatically saved for federal record keeping purposes. Staffers using that system had to formally designate individual emails for archiving and rarely did so, the watchdog found.

In 2011, “Department employees created 61,156 record emails out of more than a billion emails sent,” the report says. In 2013, even fewer emails — 41,749 — were designated for preservation.

At a news conference Tuesday, the likely presidential candidate argued that her decision to use a personal email account “for convenience” did not interfere with the department’s ability to retrieve those messages in response to Freedom of Information Act requests or for the historical record.

“The vast majority of my work emails went to government employees at their government addresses, which meant they were captured and preserved immediately on the system at the State Department,” Clinton said Tuesday.

Transparency advocates said the report undermines the former secretary’s assertion.

“Her justification around FOIA requests and around preservation became that most of the documents were cc’d or sent to .gov or state.gov addresses used by employees and therefore were preserved and accessible to requests, ” said John Wonderlich of the Sunlight Foundation. “This [report] suggests that is not reliable at all.”

In some State Department diplomatic posts and offices, trivial numbers of emails were marked as “records” to be preserved in accordance with department policies. State’s Bureau of Energy Resources designated two emails for archiving in 2013. The Population, Refugees and Migration Bureau sent seven such messages, according to the report.

It’s not clear from the report whether officials with whom Clinton traded emails were covered by the SMART system, which required message-by-message selection for archiving, or by other email systems which may have taken a more automated approach. The IG review says in a footnote that the SMART system was not used by State’s “high-level principals, the Secretary, the Deputy Secretaries, the Under Secretaries, and their immediate staffs, which maintain separate systems.”

Clinton provided 55,000 pages of emails from her private account to the State Department in December at the agency’s request. The full set of emails was not previously accessible to State when conducting records searches or for Freedom of Information Act requests, though some were discovered in email accounts belonging to other State employees.

Spokespeople for the State Department and for Clinton did not immediately respond to messages seeking comment.

It’s possible that some State officials are still archiving emails the old-fashioned way, by printing them out and putting them in paper files. The IG report did not attempt to quantify such efforts.

However, the IG report said a large number of employees seemed to be neglecting their archival duties because they did not understand them.

“Most mission and bureau employees who did not use record emails as intended told OIG they were usually unaware of what types of information should be saved as record emails,” the report said. “The Department does not give employees adequate training to distinguish between information that should be preserved as records and information that may be discarded.”

The report also said some State staffers acknowledged not marking some emails as “records” because that would make them more widely available. “Many interviewees expressed a fear that if participants in … a debate knew that their opinions would be permanently recorded or accessible in searches, they would not express their opinions in an uninhibited manner,” the report said. It was unclear whether employees feared disclosure within the department or outside of it.

One former State Department employee agreed there was widespread confusion about what email to save and what to discard.

”I think it’s an all-of-government problem with all of this stuff. People aren’t given proper instructions,” said the former official, who asked not to be named. “They don’t tell you how to manage these systems going in.”

Wonderlich noted that if every government employee assumed that every other email recipient was responsible for saving it electronically or on paper, then none of those records would be preserved.

“It’s absurd,” he said. “We don’t allow everyone to erase every message sent to their inbox simply because someone may be able to reconstruct them from emails in some other office or agency.”

In 2013, the National Archives proposed a new email archiving strategy known as Capstone, under which agencies designate official accounts of high-ranking officials or decision-makers to be permanently archived in their entirety or by default. The Capstone approach remains voluntary.

The IG report was produced between January and March of last year.