Police officers in Newport, R.I., who interviewed the man, Aaron Alexis, on Aug. 7 were concerned enough by his claims to be hearing voices sent by a "microwave machine" that they faxed their report to naval police in Newport, where Mr. Alexis was working temporarily as a contractor. The report was logged by security personnel at the station, but never made it into the hands of officials who could have revoked Mr. Alexis' security clearance to enter the navy yard, where the police say he killed a dozen civilians on Monday before the police shot him to death.
"In a big organization like the Navy it is never as connected as it should be, so you have reports and things that come into offices and never make it back to headquarters," said a former senior federal official who has been briefed on the investigation.
While working in Rhode Island for a Navy computer services contractor, Mr. Alexis, a 34-year-old former Navy reservist from Fort Worth, also complained to his employer that he was hearing voices through the walls of his hotel room and having trouble sleeping, a person with knowledge of the company said.
Human resource officials at the company, the Experts, believed Mr. Alexis was describing actual noise and twice moved him to different hotels. They were concerned enough to contact the Newport police after Mr. Alexis said he had spoken to officers. The police did not provide details of Mr. Alexis' statements about hearing voices, the person with knowledge of the company said.
The new information about the Newport Naval Station's failure to pass along the police report came hours after Defense Secretary Chuck Hagel acknowledged that the process used to grant security clearances and access to military installations was in need of review, and most likely repair, in the wake of the shootings. Mr. Hagel acknowledged that "red flags" about the gunman's past behavior were missed.
"Obviously, something went wrong," Mr. Hagel said as he announced that he had ordered reviews of physical security, access procedures and the process for granting and renewing security clearances at Defense Department installations around the world.
"Where there are gaps we will close them, where there are inadequacies we will address them, where there are failures we will correct them," he said. "Our people deserve safe and secure workplaces."
The Department of Veterans Affairs confirmed in a statement on Wednesday that Mr. Alexis visited the emergency room at a veterans' medical center in Providence, R.I., on Aug. 23, two weeks after telling the police in Newport that strangers were harassing him with a microwave machine, and that he had been hearing voices "through the wall, flooring and ceiling." But according to the statement, he told a doctor only that he was having insomnia, and he was given a "small amount" of medication, which an official said was the antidepressant Trazodone. He requested and received a refill five days later at a veterans' medical center in Washington, saying he could not sleep because of his work schedule.
Mr. Alexis apparently did not mention hearing voices. And when asked if he was experiencing anxiety or depression, or was having thoughts of hurting himself or others, he answered no. "He was alert and oriented," the statement said.
Mr. Alexis enrolled in the Veterans Affairs health system in February 2011, shortly after receiving an honorable discharge from the Navy Reserve. But he never sought an appointment from a mental health specialist, and he canceled or did not show up for scheduled primary care appointments, the statement said. He was receiving veterans' disability compensation of $395 a month for orthopedic problems and tinnitus.

Michael D. Shear contributed reporting.