Authorities in New York City and at the Social Security Administration now have explanations for why most of the 3,000 victims of the 9/11 terrorist attacks are missing from an important federal registry of deaths.

The federal government was fully informed by city officials about all of the tragic deaths — authorities agree — but was prevented from publicly releasing them because of a morass of reporting laws and restrictions.

Since few bodies were recovered from the collapsed World Trade Center’s twin towers, privately owned funeral homes did not independently report the deaths to the Social Security Administration, as is their common practice.

But these reasons raise new and troubling questions about the reliability of the Death Master File — a public record overseen by Social Security and widely used by credit agencies, banks and other business interests. The file was created in 1980 under a Freedom of Information lawsuit brought by U.S. businesses seeking protection from identity theft and consumer fraud.

The embarrassing reporting failure for 9/11 victims was uncovered by a Scripps Howard investigation that also found that nearly 32,000 living Americans have falsely been reported as dead, causing them difficulties with police, denying them credit cards and bank loans, and even hurting efforts to obtain jobs.

Although few Americans have heard of the Death Master File, it is frequently used in a variety of medical research and even determines eligibility for critically ill Americans awaiting organ transplants.

“I am very concerned that it appears that so many of those who died on 9/11 cannot be found in the Death Master File,” said Rep. Carolyn Maloney, D-N.Y. She asked for an explanation from authorities.

“The agencies responded and stated that current protocols were followed. I will be looking into what can be done to get better protections and increased accuracy,” Maloney said.

According to the official Death Master File, only 405 people died in the state of New York on Sept. 11, 2001 — just a slight increase from the state’s daily average of about 350 deaths.

New York City officials, at Maloney’s request, reviewed their records and confirmed that they had reported all of the victims of the 9/11 attacks to the federal government. “Even though all New York City deaths are reported … the deaths are not public information,” City Health Commissioner Thomas Farley said.

Social Security Administration Commissioner Michael Astrue agreed in a letter to Maloney.

“We cannot legally share all of our death information,” said Astrue. “If we received the report of death from a source other than a state (or city) government, the name of a victim could appear on the public Death Master File.”

But there were special circumstances that prevented the 9/11 deaths from getting into the Death Master File.

“In most cases there were no physical remains, so (private) funeral directors were not involved,” said Steven Schwartz, vital-records registrar for New York City.

Another non-government source of death reports are family members who are eligible to receive Social Security survivor benefits.

“In our vital-records analysis of those deaths, we determined that about 70 percent of these people were under 40,” said Susan Craig, a spokeswoman for the New York City Health Department.

Schwartz agreed.

“There is no question that these were largely younger people,” he said. “When there are younger victims, there may not be survivors” to claim federal benefits.

As a result, more than 90 percent of New York’s victims were not recorded in the Death Master File.