Former secretary of state Hillary Clinton, accompanied by Sen. Elizabeth Warren (D-Mass.), speaks to and meets Ohio voters during a rally at the Cincinnati Museum Center at Union Terminal on Monday, June 27. (Melina Mara/The Washington Post)

Ths story has been updated:

As Hillary Clinton tries to put to rest the controversy over her private email server that has dogged her presidential campaign, she has repeatedly cited her willingness to make her work correspondence public as evidence that she has nothing to hide.

“I have provided all of my work-related emails, and I’ve asked that they be made public, and I think that demonstrates that I wanted to make sure that this information was part of the official records,” she told ABC News last month.

But disclosures over the past several weeks have revealed dozens of emails related to Clinton’s official duties that crossed her private server and were not included in the 55,000 pages of correspondence she turned over to the State Department when the agency sought her emails in 2014.

At least 160 such emails have come to light so far, many of them through public-records lawsuits brought by the conservative group Judicial Watch.

In one email released by Judicial Watch on Monday, Clinton queried aide Huma Abedin and another staffer about how her official records were being maintained. “I have just realized I have no idea how my papers are treated at State. Who manages both my personal and official files?” she wrote on March 22, 2009.

A 2010 Clinton email, which was disclosed last month by the State Department’s inspector general but had not been submitted by the former secretary, appears to show that she was concerned about ensuring privacy for her personal emails if she was given an official government account.

“Let’s get separate address or device but I don’t want any risk of the personal being accessible,” Clinton wrote.

The newly disclosed gaps in Clinton’s correspondence raise questions about the process used by the presumptive Democratic presidential nominee and her lawyers to determine which emails she turned over to the department.

Clinton has said she deleted nearly 32,000 emails from her time as secretary because they were purely personal, dealing with such matters as arrangements for her daughter’s wedding and her yoga routine. But Republicans have said there is no way to know whether Clinton also deleted potentially embarrassing work-related emails.

The State Department has released redacted copies of the emails Clinton handed over. The newly disclosed emails have emerged as the agency has released copies of Abedin’s correspondence, which in some cases includes previously undisclosed exchanges with Clinton.

Brian Fallon, a Clinton campaign spokesman, said that both Clinton and Abedin provided “all potentially work-related emails in their possession” to the State Department.

Fallon added: “We understand Secretary Clinton had some emails with Huma that Huma did not have, and Huma had some emails with Secretary Clinton that Secretary Clinton did not have.”

The email controversy has haunted Clinton’s candidacy for more than a year and contributed to her rising unfavorable poll numbers. Presumptive Republican nominee Donald Trump’s negative ratings are higher, and Clinton has taken a solid lead in recent national surveys.

But the email disclosures come as part of ongoing litigation that is likely to cause Clinton’s campaign continued discomfort in coming months.

Judicial Watch was scheduled to spend seven hours on Tuesday taking sworn testimony from Abedin, a Clinton confidante and former State Department deputy chief of staff. A transcript of the session could be released as early as this week and is likely to provide new information about Clinton’s email setup. Another former top aide, Undersecretary for Management Patrick Kennedy, will be interviewed Wednesday. Judicial Watch has also requested permission to interview Clinton herself.

The group will also receive hundreds of additional pages of emails sent and received by Abedin using a personal email account routed through Clinton’s personal server. Abedin turned those records over to the State Department in 2015, and the department, in turn, is under a court order requiring that they be released to Judicial Watch in monthly batches over the next year. That process could well result in the publication of additional emails that Clinton had not provided to the State Department.

Another conservative group, Citizens United, has also been receiving documents showing how Clinton’s department operated.

On Monday, a judge ordered the State Department to turn over emails from Clinton’s scheduler for the weeks leading up to 14 foreign trips taken while Clinton was in office. The group hopes to use them to show that Clinton met with political donors while overseas and did not record the meetings on official schedules.

Meanwhile, an FBI investigation into the security of Clinton’s email server has yet to be resolved.

Clinton filed a sworn statement to a federal judge certifying that she submitted all emails in her possession that might have been federal records to the State Department in December 2014.

Her campaign has said she no longer had access to some of her emails, particularly from her first two months in office, while she was transitioning into the role and switching from an account linked to her AT&T BlackBerry to one routed through her home server. But her spokesman has not provided a full explanation for all of the gaps.

Judicial Watch President Tom Fitton said the growing number of Clinton work emails that she did not turn over undermined her vows of transparency.

“The most charitable interpretation is that the process she and her attorneys used to cull government emails from the emails she took with her didn’t work,” he said. “The less charitable interpretation is that these emails were not helpful to Mrs. Clinton, so they were not turned over.”

In a statement Monday night, the Trump campaign cited new emails released by Judicial Watch as a sign that Clinton had “lied” about turning over all her work-related correspondence. “We now know that Clinton’s repeated assertion that she turned over everything work-related from her time at the State Department is not true,” the campaign said.

In a report issued last month about Clinton’s email practices, the State Department inspector general’s office formally concluded that Clinton’s production of emails had been “incomplete.” Among the gaps, the IG found, were all emails Clinton sent and received between Jan. 21, 2009, when she took office, and March 17, 2009. The IG said emails were also missing that Clinton sent from the start of her term until April 12, 2009.

Among those the IG said she had not turned over were 19 emails exchanged with Gen. David H. Petraeus in January and February 2009. Approximately 15 additional emails that Clinton exchanged with informal adviser Sidney Blumenthal were turned over by Blumenthal to the House committee investigating the 2012 attacks on U.S. outposts in Benghazi, Libya, but did not appear among the emails she had turned over.

An additional 127 have emerged through Judicial Watch litigation, according to a new analysis by the group.

The State Department has not addressed the gaps in Clinton’s emails other than to note that it is methodically responding to public records requests as they are received, which has included releasing all of Clinton’s emails, as well as some emails from Abedin and other aides.

A steady stream of internal State Department documents released in response to public records requests promises new revelations until Election Day about Clinton’s leadership of the department.

One series of documents requested by Citizens United and then published by ABC News and other news organizations appears to show that Clinton’s top staff intervened to appoint a Democratic donor to a sensitive arms control advisory panel even though the donor, a Chicago securities trader, had no experience in the field.

The emails show that some State Department staffers were initially puzzled when they received questions regarding the appointment of Rajiv K. Fernando to the International Security Advisory Board in 2011. “The true answer,” one official wrote at the time, explaining the inclusion of Fernando on a list of candidates, is that Clinton’s chief of staff Cheryl Mills “added him.”

Fernando had also been a major donor to the Clinton Foundation, the global charity started by former president Bill Clinton. He resigned the board position shortly after ABC News inquired about the appointment in 2011.

Clinton campaign spokesman Nick Merrill noted the board was a volunteer advisory panel, its charter called for members with a diverse set of experiences, and that this was one of several foreign policy-oriented organizations with which Fernando was involved.

Fernando could not be reached for comment.

This story has been updated to reflect a new analysis from the conservative group Judicial Watch.