NEW YORK (Reuters) - The U.S. State Department released the final batch of Hillary Clinton’s emails on Monday from her time at the agency’s helm, bringing the final tally of emails it says contain classified information to more than 2,000. The department has been regularly releasing batches of her work emails in keeping with a judge’s order. But Monday’s release of the final 1,700 messages does not end the controversy and legal uncertainty dogging Clinton’s Democratic presidential campaign since her use of a private email server came to light a year ago. Republican rivals in the battle for the Nov. 8 election have cited the email controversy in saying Clinton, the Democratic front-runner, is unfit for the presidency. Clinton, secretary of state from 2009 to 2013, has said her email arrangement broke no rules and that she will be vindicated. One of the newly released exchanges shows Clinton and Jake Sullivan, one of her closest aides, in a discussion now entirely censored as “secret,” the second-highest level in the government’s three-tier classification system.  The messages, sent on June 7, 2012, bear the subject “Khar - where we are” - likely a reference to Hina Rabbani Khar, Pakistan’s foreign minister. The previous day, Pakistan had renewed its insistence that the United States apologize for an air attack that killed 24 Pakistani soldiers. All told, classified information appears in 2,093 of the 30,300 work emails and attachments Clinton’s lawyers returned to the department in 2014, including 261 such emails released on Monday. That information is obscured with white boxes in the public copies.  The government forbids sending or storing classified information outside secure, government-controlled channels. The FBI has taken the server and is investigating with U.S. Justice Department attorneys whether laws were broken through the unusual arrangement. The State Department’s inspector general and at least two Republican-led congressional committees are conducting similar inquiries.  The State Department is investigating how much of the information in the more than 2,000 emails marked as classified was classified at the time they were sent. The vast majority of those messages - 2,028 - contain information classified at the “confidential” level, the lowest, including scores sent by Clinton herself. A further 65 contain “secret” information, including at least one written by Clinton, while 22 contain “top-secret” information from U.S. intelligence agencies, which have been entirely withheld from release. Members of the public are still fighting the department in court for access to thousands of public records connected to some of Clinton’s closest aides. Last week, a federal judge granted a request by a conservative group suing the State Department under open records laws to seek sworn testimony from department officials and Clinton aides to see if the arrangement was intended to thwart public access to government records. Clinton’s staff has accused the government of overclassifying, and attribute the large number of emails now marked as classified to an “interagency” dispute between the State Department and intelligence agencies. At most, only a few dozen of the 2,000 classified emails included information from intelligence agencies, according to several people familiar with those agencies’ analyses of the emails. The vast majority of the classified information originated with State Department ambassadors and employees, including Clinton herself. State Department lawyers told a federal judge last week they still did not know who in the government authorized Clinton’s email arrangement or why. Clinton has said the arrangement was for her convenience, but that she now regrets it. The Justice Department, seeking to rebut suggestions that President Barack Obama’s administration may have inappropriate influence on its investigation, has not briefed the White House on its progress, Attorney General Loretta Lynch said on Monday.  (Reporting by Jonathan Allen; Additional reporting by Mark Hosenball and Idrees Ali; Editing by Andrea Ricci and Peter Cooney) This article was funded in part by SAP. It was independently created by the Reuters editorial staff. SAP had no editorial involvement in its creation or production.