The unclassified version of the report, released late on Tuesday by the State Department, concluded that the mission was completely unprepared to deal with a September 11 attack that killed US Ambassador Chris Stevens and three other Americans.
Responsibility for security shortcomings in Benghazi lay farther down the State Department command chain, said Retired Ambassador Thomas Pickering, who lead the inquiry.
"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.
A deputy assistant secretary in the Bureau of Near Eastern affairs resigned after the report, a Capitol Hill source said. Media outlets reported other resignations, including Eric Boswell, the assistant secretary of state for diplomatic security, one of his deputies and another official.
State Department officials declined to comment.
The report by the Accountability Review Board probing the attack and comments by its two lead authors suggested that Clinton, who accepted responsibility for the incident, would not be held personally culpable.
"The secretary of state has been very clear about taking responsibility here, it was from my perspective not reasonable in terms of her having a specific level of knowledge," said retired Admiral Michael Mullen, the former chairman of the US Joint Chiefs of Staff and the other inquiry leader.
Pickering and Mullen spoke to the media after briefing members of the House 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 and will instead be represented by her top two deputies.
The unclassified version of the report 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 scathing report could tarnish Clinton's four-year tenure as secretary of state, which has seen her consistently rated as the most popular member of President Barack Obama's Cabinet.
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 US facilities.
The National Defense Authorization Act for 2013, which is expected to go to Congress for final approval this week, includes directing the Pentagon increase the Marine Corps presence at diplomatic facilities by up to 1,000 Marines.
Some Capitol Hill Republicans who had criticised the Obama administration's handling of the Benghazi attacks said they were impressed by the report.
"It was very thorough," said Senator Johnny Isakson. Another Republican, 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.
But Republicans continued to call for Clinton to testify as soon as she is able.
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.
"I do think it's imperative for all concerned that she testify in an open session prior to any changing of the regime," Corker said.
Republicans have focused much of their firepower on US Ambassador to the United Nations Susan Rice, who appeared on television 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 for the State job, withdrew her name from consideration last week.