This is a significant turnaround of the previous version of the attack coming from the Obama Administration that this was a spontaneous protest against an anti-Islam video.
The attack resulted in the death of four Americans including the US Ambassador to Libya.
"As we learned more about the attack, we revised our initial assessment to reflect new information indicating that it was a deliberate and organized terrorist attack carried out by extremists," Shawn Turner, the spokesman for the Director of National Intelligence, said in a statement.
"It remains unclear if any group or person exercised overall command and control of the attack, and if extremist group leaders directed their members to participate. However, we do assess that some of those involved were linked to groups affiliated with or sympathetic to al-Qaeda," he said.
In the unusual statement 17 days after the terrorist attack on US personnel and facilities in Benghazi, Turner said the Intelligence Community launched a comprehensive effort to determine the circumstances surrounding the assault and to identity the perpetrators and reviewed all available intelligence to determine if there might be follow-on attacks against US people or facilities in Libya or elsewhere.
In the immediate aftermath of the attack on the Benghazi Consulate, the statement said, there was information that led the intelligence community to assess that the attack began spontaneously following protests earlier that day at US Embassy in Cairo.
"We continue to make progress, but there remain many unanswered questions. As more information becomes available our analysis will continue to evolve and we will obtain a more complete understanding of the circumstances surrounding the terrorist attack," he added.
DNI, Turner said, continues to support the ongoing FBI investigation and the State Department review of the Benghazi terrorist attack, providing the full capabilities and resources of the Intelligence Community to those efforts.
The DNI statement comes days after the US Ambassador to the UN, Susan Rice, had termed the attack as a result of the spontaneous protest.
Rice's defended her earlier statement given to Sunday talk shows.
"Ambassador Rice's comments were prefaced at every turn with a clear statement that an FBI investigation was under way that would provide the definitive accounting of the events that took place in Benghazi," her spokeswoman Erin Pelton said in a statement.
Following the DNI statement, Congressman Peter King, chairman of the House Committee on Homeland Security, demanded resignation of Rice. "I think we have to show that there is a price to be paid for such a gross misstatement of reality," King told CNN in an interview.
Senator John Kerry, chairman of the Senate Foreign Relations Committee, defended Rice's statement.
"I'm deeply disturbed by efforts to find the politics instead of finding the facts in this debate. Everyone who cares about the five fallen Americans in Benghazi would do well to take a deep breath about what happened and allow Secretary Clinton's proactive, independent investigation to proceed. I'm particularly troubled by calls for Ambassador Rice?s resignation," he said.
"She is a remarkable public servant for whom the liberation of the Libyan people has been a personal issue and a public mission. She's an enormously capable person who has represented us at the United Nations with strength and character," Kerry said in a statement.