"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.
The station cited an unnamed law enforcement source as saying the team was less than 30 seconds from the base gate when the first call went out alerting police of the shooting.
The team was preparing to enter the facility in a bid to stop the gunman when the commander called them back to the Capitol, the station reported without attribution.
While Alexis' employer, an information technology contractor called The Experts, said it had no reports of trouble with him from Navy bases where he had worked over the summer, a picture was building of an increasingly troubled mind.
On August 7, Alexis told police in Newport, Rhode Island, that he believed he was being followed by three people who had been dispatched by someone with whom he'd quarreled, a police report said.
He said they had been sent to "follow him and keep him awake by talking to him and sending vibrations into his body," according to the report.
Alexis said he hadn't seen any of these people, but insisted they'd followed him between three hotels in the area -- the last being a Marriott, where police investigating a harassment complaint stopped to talk with him.
There, Alexis told authorities the unseen individuals continued speaking to him through walls and the floor. He said they used "some sort of microwave machine" to send vibrations into his body to keep him awake.
He added, according to the police report, that "he does not have a history of mental illness in his family and that he never had any sort of mental episode." Nonetheless, a police sergeant alerted authorities at Naval Station Newport to Alexis "hearing voices." Reached Tuesday, officials at the base referred CNN to the FBI, which declined to comment.
Benita Bell met Alexis last week at the Residence Inn where he was staying before the shootings.