Pierson has been under pressure since it came to light that an alleged fence-jumper made it further into the White House than previously reported. The Secret Service had originally said the man was caught while entering the building, but later confirmed reports that he had made it all the way to the East Room.
At a congressional hearing on Tuesday, she admitted that there had been mistakes in the execution of the agency's "security plan."
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"Today Julia Pierson, the director of the United States Secret Service, offered her resignation, and I accepted it. I salute her 30 years of distinguished service to the Secret Service and the nation," Department of Homeland Security Secretary Jeh Johnson said in a statement, adding that he has directed Deputy Secretary of Homeland Security Alejandro Mayorkas "to assume control and direction of the ongoing inquiry" into the alleged fence-jumper.
Johnson also said that he will convene an independent panel of experts to make its own assessments and recommendations based on the Sept. 19 fence-jumping incident.
After the Tuesday testimony, high-ranking lawmakers from both parties—including Sen. Chuck Schumer, the No. 3 Senate Democrat, and Sen. Lindsey Graham, a Republican—had signaled that Pierson should resign. House Speaker John Boehner did not directly call for her resignation, but said he would support an independent investigation.
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News outlets reported Wednesday morning that another security lapse had occurred when an armed guard had ridden in an elevator with the president without the Secret Service's knowing about the weapon.
—The Associated Press contributed to this report.