Morell retired after 33 years at the CIA, including two stints as acting director and one as deputy director.
"I was most looking forward to ... the opportunity to work side-by-side once again with Michael Morell," said Brennan, noting that they'd begun their careers at the CIA in 1980. "As much as I would selfishly like to keep Michael right where he is for as long as possible, he has decided to retire to spend more time with his family and to pursue other professional opportunities."
Brennan said Morell, 54, will be replaced by Avril Haines, 43, the first woman to hold that position. Haines has been a White House deputy assistant and deputy counsel for national security affairs since 2010. Before that, she was assistant legal adviser for treaty affairs at the State Department, according to a White House statement.
Obama has appointed Morell to the President's Intelligence Advisory Board, a group of mostly retired people who help advise the White House on intelligence policy.
Morell made the final edit on the memo of talking points on the attack last year that killed four Americans in Benghazi, including Ambassador Chris Stevens. Emails exchanged by administration officials that week show Morell deleted references to the CIA warning the State Department of previous militant attacks in Benghazi.
U.N. Ambassador Susan Rice used those notes on Sunday talk shows, triggering an ongoing controversy in which House Republicans accuse the administration of covering up any connections to terror groups in the attack.
Rice was named national security adviser last week, replacing long-serving staffer Tom Donilon as part of the Obama administration's second-term turnover of its national security team.
During Morell's tenure as the CIA's acting director, some lawmakers criticized him for stating that the CIA's interrogation program produced some useful information. Morell had said in a statement to CIA employees that while the film "Zero Dark Thirty" was wrong to depict harsh techniques as key to finding Osama bin Laden, those interrogations did produce some useful intelligence.
"Some came from detainees subjected to enhanced techniques, but there were many other sources as well," Morell said.
A Senate Intelligence Committee investigation into the CIA's detainee interrogati on program completed last December concluded that interrogation methods such as waterboarding produced no useful intelligence.
In a letter to Morell, Senate Intelligence Committee Chairwoman Dianne Feinstein and other lawmakers asked Morell to back up his claim and to cite what information was acquired from CIA detainees and when. "Prior to, during, or after the detainee was subjected to the CIA's enhanced interrogation techniques? If after, how long after?" the letter said.
The senators contended that that the CIA detainee who provided the most accurate information about the courier who was tracked to bin Laden's hiding place "provided the information prior to being subjected to coercive interrogation techniques."