WASHINGTON (AFP) - The mother of the defence contractor who gunned down 12 people at the Washington Navy Yard apologised on Wednesday for her son's rampage and said she did not understand his actions.

"To the families of the victims, I am so, so very sorry that this has happened. My heart is broken," Cathleen Alexis said in a statement that she read to the media at her home in Brooklyn, New York.

Her comments were aired on US news networks including CNN.

Aaron Alexis, 34, opened fire Monday at the tightly guarded Washington Navy Yard, for which he had a valid entry pass, according to the FBI.

He eventually died in a shootout with police at the giant compound in the heart of the US capital.

"Aaron is now in a place where he can no longer do harm to anyone, and for that I am glad," his mother said.

"I don't know why he did what he did, and I'm never going to be able to ask him why." Two days after the shooting, officials were still searching for answers as to why Alexis, a former sailor with a history of disciplinary problems and brushes with the law, went on the rampage.

They also questioned how he had been granted a security clearance.

US Defence Secretary Chuck Hagel acknowledged on Wednesday that authorities missed some "red flags" ahead of the deadly mass shooting.

Media reports have suggested that Alexis was delusional, but Pentagon officials could not confirm if he suffered mental health problems.

Cathleen Alexis told CNN that she had not been able to leave her home since Monday afternoon.

In the wake of the incident, US President Barack Obama has called once again on Congress to act on stalled gun reform measures.