Trump also restored top U.S. intelligence officials as permanent members, according to the filing signed Tuesday and announced Wednesday.
The Joint Chiefs of Staff chairman, Marine Corps Gen. Joseph Dunford, and Director of National Intelligence Dan Coats returned to their roles on the committee, the filing said. The director of the Central Intelligence Agency, Mike Pompeo, also becomes a permanent member of the principals committee.
Bannon, who formerly was executive chairman of Breitbart News Network, was elevated to the position on Jan. 28, eight days after Trump became president.
Sean Spicer, the White House press secretary, at the time said Bannon's experience as "a former naval officer" offers knowledge and experience.
Bannon's "got a tremendous understanding of the world and the geopolitical landscape that we have now," Spicer said. "Having the chief strategist for the president in those meetings, who has a significant military background, to help make, guide what the president's final analysis is going to be is crucial."
Trump fired Flynn on Feb. 13 after not disclosing to the president or to Vice President Mike Pence the extent of his conversations with Sergey Kislyak, Russia's ambassador to the United States.
Trump replaced Flynn with Gen. H.R. McMaster.
"Susan Rice operationalized the NSC during the last administration," Bannon said in a statement, referring to the national security adviser under the Obama administration. "I was put on to ensure that it was de-operationalized. Gen. McMaster has returned the NSC to its proper function."
A Quinnipiac poll released Tuesday showed that 11 percent of those surveyed had a favorable opinion of Bannon and 45 percent an unfavorable view. Trump has 35 percent approval and 57 percent disapproval in the poll.
McMaster was given responsibility for setting the agenda for the NSC or the Homeland Security Council meetings and can delegate that authority to Homeland Security Adviser Tom Bossert, according to the filing.
According to the memorandum, the principals committee "shall continue to serve as the Cabinet-level senior interagency forum for considering policy issues that affect the national security interests of the United States."