Eric Boswell has resigned effective immediately as assistant secretary of state for diplomatic security, State Department spokeswoman Victoria Nuland said in a terse statement. A second official, speaking on condition of anonymity, said Boswell had not left the department entirely and remained a career official.
Nuland said that Boswell, and the three other officials, had all been put on administrative leave "pending further action."
An official panel that investigated the incident concluded that the Benghazi mission was completely unprepared to deal with the attack, which killed U.S. Ambassador Christopher Stevens and three other Americans.
The unclassified version of the report, which was released on Tuesday, cited "leadership and management" deficiencies, poor coordination among officials and "real confusion" in Washington and in the field over who had the authority to make decisions on policy and security concerns.
"The ARB identified the performance of four officials, three in the Bureau of the Diplomatic Security and one in the Bureau of (Near Eastern) Affairs," Nuland said in her statement, referring to the panel known as an Accountability Review Board.
Secretary of State Hillary Clinton accepted Boswell's decision to resign effective immediately, the spokeswoman said.
Earlier, a U.S. official who spoke on condition of anonymity said Boswell, one of his deputies, Charlene Lamb, and a third unnamed official has been asked to resign. The Associated Press first reported that three officials had resigned.
PANEL STOPS SHORT OF BLAMING CLINTON
The Benghazi incident appeared likely to tarnish Clinton's four-year tenure as secretary of state but the report did not fault her specifically and the officials who led the review stopped short of blaming her.
"We did conclude that certain State Department bureau-level senior officials in critical positions of authority and responsibility in Washington demonstrated a lack of leadership and management ability appropriate for senior ranks," retired Admiral Michael Mullen, one of the leaders of the inquiry, told reporters on Wednesday.
The panel's chair, retired Ambassador Thomas Pickering, said it had determined that responsibility for security shortcomings in Benghazi belonged at levels lower than Clinton's office.
"We fixed (responsibility) at the assistant secretary level, which is, in our view, the appropriate place to look for where the decision-making in fact takes place, where - if you like - the rubber hits the road," Pickering said after closed-door meetings with congressional committees.
The panel's report and the comments by its two lead authors suggested that Clinton, who accepted responsibility for the incident in a television interview about a month after the Benghazi attack, would not be held personally culpable.
Pickering and Mullen spoke to the media after briefing members of the House of Representatives Foreign Affairs Committee and Senate Foreign Relations Committee behind closed doors on classified elements of their report.
Clinton had been expected to appear at an open hearing on Benghazi on Thursday, but is recuperating after suffering a concussion, dehydration and a stomach bug last week. She will instead be represented by her two top deputies.
Clinton, who intends to step down in January, said in a letter accompanying the review that she would adopt all of its recommendations, which include stepping up security staffing and requesting more money to fortify U.S. facilities.
The National Defense Authorization Act for 2013, which is expected to go to Congress for final approval this week, includes a measure directing the Pentagon to increase the Marine Corps presence at diplomatic facilities by up to 1,000 Marines.
Some Capitol Hill Republicans who had criticized the Obama administration's handling of the Benghazi attacks said they were impressed by the report.
"It was very thorough," said Senator Johnny Isakson. Senator John Barrasso said: "It was very, very critical of major failures at the State Department at very high levels." Both spoke after the closed-door briefing.
Others, however, took a harsher line and called for Clinton to testify as soon as she is able.
"The report makes clear the massive failure of the State Department at all levels, including senior leadership, to take action to protect our government employees abroad," Representative Mike Rogers, the Republican chairman of the House Intelligence Committee, said in a statement.
Senator Bob Corker, who will be the top Republican on the Senate Foreign Relations Committee when the new Congress is seated early next year, said Clinton should testify about Benghazi before her replacement is confirmed by the Senate.
Republicans have focused much of their firepower on U.S. Ambassador to the United Nations Susan Rice, who appeared on TV talk shows after the attack and suggested it was the result of a spontaneous protest rather than a premeditated attack.
The report concluded that there was no such protest.
Rice, widely seen as President Barack Obama's top pick to succeed Clinton, withdrew her name from consideration last week.