The emails former Secretary of State Hillary Rodham Clinton turned back over to the government last year contained “gaps,” according to internal department messages evaluating her production.

Mrs. Clinton took office on Jan. 21, 2009, but the first message she turned back over to the department was dated March 18, and the earliest-dated message she herself sent was on April 13, or nearly three months into her time in office, according to a message obtained through an open records request by Judicial Watch, which released it Monday.

Mrs. Clinton has said she continued using a previous account she’d used during her time as a senator for business at the beginning of her time as secretary, but the differing dates between the first email received and the first sent raise still more questions.

The revelation of the gap comes even as the legal situation grows more complicated.

Two Senate committee chairmen pushed Monday to try to find out just how deeply the Justice Department’s investigation into the Clinton email server has gone, as the two senators tried to figure out ways of getting Bryan Pagliano, the tech staffer who helped set up her email server at her home in New York, to spill what he knows.

In a letter to Attorney General Loretta E. Lynch, Sens. Chuck Grassley and Ron Johnson asked the government to say whether it would object to a “proffer” session between the senators and Mr. Pagliano, where he could detail, off the record, what he knows without having to worry about it being used against him in a prosecution.

Meanwhile, the State Department met with more resistance from the myriad groups who have sued to pry loose emails from Mrs. Clinton and her top aides, and who told a federal court Monday they don’t want to see the proceedings centralized in a single judge.

“State should have anticipated many years ago that it would experience an increase in [Freedom of Information Act] requests for records about Mrs. Clinton’s tenure as secretary of state, and planned accordingly. Yet apparently nothing was done at any time in the last six years to prepare for this highly foreseeable expense, and state now relies on its own failure to prepare as justification to delay complying with its obligations under FOIA,” Jason Leopold, a journalist whose case has prompted the ongoing release of Mrs. Clinton’s emails, said in a court filing made by his lawyer.

Mrs. Clinton declined to use the State Department’s regular email system during her time in office, instead setting up a server at her home and using an account on that server. Many of her top aides also used personal accounts or accounts on the server Mrs. Clinton kept.

Mrs. Clinton says she didn’t break any laws, though the State Department and at least one federal judge have said she violated policy. And the use of non-State.gov accounts has shielded much of the information from subpoenas, congressional inquiries and open records requests — until now.

The State Department would like to shield them a little longer, having asked the federal district court to consolidate more than 30 search lawsuits that have been filed.

Several judges have already indicated they’ll object to that, however, and have turned down delay requests in the meantime. The judges are also pushing the State Department to be more forthcoming in how many emails it is sitting on from Mrs. Clinton’s aides.

The revelation of a possible email gap in Mrs. Clinton’s own records came out of the State Department’s response to one of the open records cases.

According to Eric F. Stein, a State Department official who wrote the evaluation of Mrs. Clinton’s messages, there were “gaps” of several weeks at the beginning and end of her records.

For example, the last message she turned over was dated on her last day in office, Feb. 1, 2013, and it came from Cheryl Mills, one of her top aides. But the last message Mrs. Clinton herself sent and turned over was dated Dec. 30, 2012, a month before she left office.

Mrs. Clinton’s presidential campaign didn’t respond to a request for comment about the email gap, but the State Department, in a statement, said Mr. Stein’s evaluation was later proved wrong and the department found emails from Mrs. Clinton’s last days in office, so there is no gap then.

“We are not aware of any gaps in the Clinton email set, with the exception of the first few months of her tenure when Sec. Clinton used a different email account that she advised she no longer has access to,” the department said. “There is no ‘gap’ in Secretary Clinton’s sent messages from … December 2012 through the end of January 2013. Upon review, the department has many messages sent by Secretary Clinton during that period, including messages that appear to have been produced directly from her ‘sent’ mailbox. Future document releases will include emails from this time period.”

Judicial Watch, a conservative public interest law firm that has filed 20 separate open records lawsuits demanding release of emails from Mrs. Clinton or her aides, said the gaps could contradict Mrs. Clinton’s assertion, under penalty of perjury, when she said she returned all work-related emails that were on the server she kept at her New York home.

“The Obama administration and Hillary Clinton have taken their cover-up of the email scandal too far,” said Tom Fitton, president of Judicial Watch. “I suspect that federal courts will want more information, under oath, about the issues raised in these incredible documents.”

The emails obtained by Judicial Watch give more details about the documents Mrs. Clinton turned over — 55,000 printed pages, divided into 12 boxes.

One March 23, 2015, a letter to Mrs. Clinton’s personal lawyer, David E. Kendall, detailed the department’s early thoughts about the documents.

The State Department asked that any of the emails still in electronic format be preserved, warned that some of the documents could be deemed classified and said Mrs. Clinton would need permission before releasing any of the documents.

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