Obama administration officials said those who had stepped down were Eric Boswell, the assistant secretary of state for diplomatic security, Charlene Lamb, the deputy assistant secretary responsible for embassy security, and Raymond Maxwell, the deputy assistant secretary of state who oversees Libya, Algeria, Tunisia and Morocco. The officials spoke on condition of anonymity because they weren't authorized to discuss personnel matters publicly.
The official added that some of the three may have the option of being reassigned to other duties.
The State Department declined immediate comment on the resignations. The officials' decisions had been criticized in the unclassified version of the Accountability Review Board's report that was released Tuesday.
That board's co-chairman, retired Adm. Mike Mullen, told reporters that the board had not determined that any officials had "engaged in willful misconduct or knowingly ignored his or her responsibilities."
However, Mullen added, "We did conclude that certain State Department bureau level senior officials in critical levels of authority and responsibility in Washington demonstrated a lack of leadership and management ability appropriate for senior ranks in their responses to security concerns posed by the special mission."
Mullen said security in Benghazi fell through bureaucratic cracks caused in part because buildings were categorized as temporary. According to the report, constraints had caused some officials to be more concerned with saving scarce money than in security.
Co-chairman Thomas Pickering, who is a retired ambassador, said although the personnel on the ground in Benghazi had reacted with bravery and professionalism, the security precautions were "grossly inadequate" and the contingent was overwhelmed by the heavily armed militants.
After Mullen and Pickering spoke to member of Congress in private, lawmakers from both parties had harsh words for the State Department, many saying they flat-out failed.
House and Senate negotiators working on a defense bill agreed on Tuesday to fund 1,000 more Marines at embassy security worldwide.
The Accountability Review Board's report specifically criticized the Bureau of Diplomatic Security and the Bureau of Near East Affairs. The report stated a lack of cooperation and confusion over protection at the mission in Benghazi.
However, the report broke little new ground about the timeline of the Benghazi attack. U.S. Ambassador Chris Stevens, information specialist Sean Smith, and former Navy SEALs Glen Doherty and Tyrone Woods were killed in the attack, which occurred on the 11th anniversary of Sept. 11, 2001.
The report did confirm there was no protest outside the facility, contrary to initial accounts.
Immediately following the attack, officials linked the attack to the spreading protests that started in Egypt over an American-made, anti-Islamic film. Those comments came after evidence already pointed to a distinct militant attack in Benghazi.
U.N. Ambassador Susan Rice appeared on numerous TV talk shows the Sunday after the attack and used the administration talking points linking it to the film. Much criticism over Rice's handling of the incident led her to withdraw her name from consideration to replace Hillary Rodham Clinton as secretary of state in President Barack Obama's second term.
Also, the report discounted rumors that officials in Washington had refused appeals for additional help after the attack had begun.
The Associated Press contributed to this report.