Cathleen Alexis read a statement at her home in Brooklyn, saying she is "so, so very sorry that this has happened."
She said she did not why her son did what he did, but she was glad he can no longer do harm to anyone.
"His actions have had a profound and everlasting effect on the families of the victims," she said. "To the families of the victims, I am so, so very sorry that this happened."
Her statement concluded with, "My heart is broken."
Aaron Alexis opened fire at the Navy Yard on Monday, killing 12 people and wounding eight others. He was killed in a shootout with police.
President Barack Obama plans to attend a memorial service on Sunday for the victims of the mass shooting, the White House said. Details about when and where the memorial will take place have not yet been announced.
During a news briefing Wednesday morning, Defense Secretary Chuck Hagel said there were "a lot of red flags" about Aaron Alexis' behavior that were missed.
While Hagel didn't assign blame, he announced a series of reviews in the wake of the shooting.
Police reports from around the country showed Aaron Alexis had exhibited a pattern of angry outbursts and disturbing behavior over the past decade. Authorities say the former full-time Navy reservist had been suffering a host of serious mental problems including paranoia and a sleep disorder.
Last month, he called police in Newport, R.I., saying he switched hotels three times because he heard voices in the walls and ceilings. Police documents show he wanted to file a harassment report because the voices were trying to keep him awake. Newport authorities contacted Naval station police, but they determined that he was not a threat to himself or others.
A motive for the attack has not yet been determined. His father says Alexis suffered from post traumatic stress disorder after helping to rescue people during the Sept. 11 attacks.
ABC News and The Associated Press contributed to this report.