Documents confirm Hillary Clinton was using her secret email server before the March 18 start date she previously claimed, and the State Department had access to some of the messages all along but didn’t notice, a conservative legal watchdog said Thursday.

Judicial Watch, which has filed a host of lawsuits to try to pry loose Mrs. Clinton’s emails, released a Feb. 13 exchange between Mrs. Clinton, the new secretary of state, and aide Cheryl Mills concerning Mrs. Clinton’s desire for a secure BlackBerry to handle classified email traffic.

Last year, Mrs. Clinton indicated she started using her secret account on the clintonemail.com server she kept at her home in New York in March, two months after she was sworn in as secretary.

But the email discovery confirms reports last year that she was using the account before that date. She emailed David H. Petraeus, who was serving as CIA director, from her secret account that January.

The email released Thursday by Judicial Watch was sent to Ms. Mills at her official State Department address, meaning the department has had it in its possession all along — though it did not provide it to the conservative legal group until last week.

“It’s another dirty little secret that the State Department hoped nobody would notice,” said Tom Fitton, president of Judicial Watch, who has filed a lawsuit demanding that the department go back and search for more such emails.

Mrs. Clinton had said all of the official record emails from her first two months as secretary, which she was required by law to store and leave in the department archives, are no longer available to her. But the Mills email shows the State Department itself may be sitting on a number of those messages.

The department did not comment on whether it would go back to look for more Clinton emails. Last month, it finished processing some 30,000 messages Mrs. Clinton did return to the government nearly two years after she left office.

Mrs. Clinton’s presidential campaign didn’t respond to a request seeking comment on the discrepancy in her email use.

The State Department has acknowledged gaps in records of Mrs. Clinton’s communications — particularly at the start of her tenure. An official said Thursday that the department is relying on Mrs. Clinton’s own representations about her account use.

“Secretary Clinton and her team have indicated that they provided the department with all work-related emails in her possession from her time at the department,” the official said.

The FBI and the State Department’s inspector general are looking into Mrs. Clinton’s email server and whether classified information was sent or received. Mrs. Clinton initially said no classified business was transacted, but revised her statement to say none of the information was marked classified at the time she first handled it.

A number of emails have shown, however, that she was aware of the potential for classified information to come across her email. The messages released Thursday by Judicial Watch detail the efforts her team made to try to get a secure BlackBerry device from the National Security Agency.

“The email shows there’s no doubt Mrs. Clinton was involved in the BlackBerry matter, and everything her staff knew, she knew — meaning the BlackBerrys weren’t secure, and she shouldn’t be using them,” Mr. Fitton said.

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