"I'm so, so very sorry this has happened. My heart is broken," she said.
Meanwhile, hospital officials said one of the three hospitalized victims of the attack had been released. The woman had been injured by a bullet that struck behind her ear, doctors previously said.
Two other people -- a civilian and a Washington police officer -- remain hospitalized in fair condition, doctors said. The officer, Scott Williams, is believed to have fired the shot that killed Alexis, ending his rampage.
Vice President Joe Biden arrived Wednesday at MedStar Washington Hospital Center to visit those injured in the shooting.
The White House announced President Barack Obama will attend a memorial service for the victims at the Navy Yard on Sunday.
"The president will want to mourn the loss of these innocent victims and share in the nation's pain in the aftermath of another senseless mass shooting," White House spokesman Jay Carney said.
Also Wednesday, Navy officials allowed employees back on the base to pick up personal belongings, Capt. Monte Ulmer, commander of Naval Support Activity Washington, told CNN affiliate WJLA. It was scheduled to resume normal operations on Thursday, he said.
The facility remained otherwise closed except for a handful of mission-essential workers.
Investigators scour crime scene, hotel and beyond
Authorities say Alexis entered the Navy Yard on Monday morning using a valid identification card. He went into Building 197, where the killings took place, carrying a bag that may have contained a disassembled shotgun, a federal law enforcement source said. Surveillance video shows him walking into a bathroom in the building and coming out with the shotgun, the official said.
Two days before Monday's shooting, Alexis spent "a couple hours" shooting at Sharpshooters Small Arms Range in northern Virginia before paying $419 for a Remington 870 shotgun and a small amount of ammunition, said the store's attorney, J. Michael Slocum. Alexis passed a federal background check for the purchase, Slocum said.
While authorities have provided few details of what happened inside Building 197, witnesses reported seeing what appeared to be a determined gunman taking aim at seemingly random victims.
Federal law enforcement sources say authorities recovered three guns from the scene: a shotgun and two handguns. The two handguns, sources say, may have been taken from guards at the naval base.
FBI teams remained at the base Wednesday amid a nationwide investigation that U.S. Attorney Ronald Machen said could take "weeks and months."
The damage inside Building 197 is significant, according to two Navy officials. There are bullet holes and broken doors and windows. There are also paint markings from law enforcement as they cleared certain areas.
"There is blood everywhere. There is damage everywhere," said one of the officials.
Tactical officers with the U.S. Capitol Police attempting to help stop the deadly rampage Monday were told by a watch commander to return to their position at the Capitol, CNN has learned.
In a statement, the agency said its officers had "offered and provided mutual support and assistance," adding that Chief Kim Dine had opened an investigation.
CNN affiliate WUSA first reported on the controversy.