The state department said diplomatic security chief Eric Boswell resigned and three other unnamed officials had been put on administrative leave.
US envoy to Libya Christopher Stevens and three other officials were killed in the attack on September 11.
An internal report said “grossly inadequate” security led to the deaths.
However, the report did not suggest disciplinary action be taken against any individuals.
“The Accountability Review Board identified the performance of four officials, three in the Bureau of the Diplomatic Security and one in the Bureau of Near East Asia Affairs,” state department spokeswoman Victoria Nuland said in a statement.
“The secretary has accepted Eric Boswell’s decision to resign… The other three individuals have been relieved of their current duties.”
US media have named one of Eric Boswell’s deputies, Charlene Lamb, and Raymond Maxwell, deputy assistant secretary for the Maghreb, among those relieved of their duties.
Christopher Stevens died of smoke inhalation when he was trapped alone in the burning building after armed men had stormed the compound.
Days after the attack, US ambassador to the UN Susan Rice said the attack seemed to have developed out of protests over an anti-Islamic film.
But later intelligence reports suggested it was a planned attack by Islamist gunmen.
Susan Rice was forced to pull out of the race to be the next secretary of state after being subjected to widespread criticism.
The board’s report found “a lack of transparency, responsiveness, and leadership” among certain senior state department officials.
But the review found no “reasonable cause” that any specific individuals had “engaged in misconduct or willfully ignored” their responsibilities.
It also said there had been “no immediate, specific” intelligence about the September 11 attack or threats to the consulate.
The probe concluded that the US personnel had “performed with courage and readiness to risk their lives to protect their colleagues in a near-impossible situation”.
But the Benghazi mission had nevertheless been hampered by a lack of resources.
Its reliance on armed “but poorly skilled” local militiamen and contract guards was “misplaced”, the report said.
In a letter to Congress, US Secretary of State Hillary Clinton said she accepted all 29 of the recommendations put forward in the report.
Hillary Clinton outlined some steps the agency would take, including sending hundreds of US Marines guards to missions abroad and assigning a state department official to oversee “high-threat posts”.
In addition, Hillary Clinton said the state department would request more funding from Congress to make improvements to security.
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