Regulations from the National Archives and Records Administration at the time required that any emails sent or received from personal accounts be preserved as part of the agency’s records.

But Mrs. Clinton and her aides failed to do so.

How many emails were in Mrs. Clinton’s account is not clear, and neither is the process her advisers used to determine which ones related to her work at the State Department before turning them over.

“It’s a shame it didn’t take place automatically when she was secretary of state as it should have,” said Thomas S. Blanton, the director of the National Security Archive, a group based at George Washington University that advocates government transparency. “Someone in the State Department deserves credit for taking the initiative to ask for the records back. Most of the time it takes the threat of litigation and embarrassment.”

Mr. Blanton said high-level officials should operate as President Obama does, emailing from a secure government account, with every record preserved for historical purposes.

“Personal emails are not secure,” he said. “Senior officials should not be using them.”

Penalties for not complying with federal record-keeping requirements are rare, because the National Archives has few enforcement abilities.

Mr. Merrill, the spokesman for Mrs. Clinton, declined to detail why she had chosen to conduct State Department business from her personal account. He said that because Mrs. Clinton had been sending emails to other State Department officials at their government accounts, she had “every expectation they would be retained.” He did not address emails that Mrs. Clinton may have sent to foreign leaders, people in the private sector or government officials outside the State Department.

The revelation about the private email account echoes longstanding criticisms directed at both the former secretary and her husband, former President Bill Clinton, for a lack of transparency and inclination toward secrecy.