A former deputy director of the Metropolitan Transportation Authority said yesterday that the agency has put riders at risk by not moving fast enough to secure underwater tunnels and other critical infrastructure.

Before taking his concerns public, the former MTA official, Nicholas Casale, wrote a letter to Mayor Bloomberg and the secretary of the federal Department of Transportation, Norman Mineta, in February, after the Chambers Street subway fire, warning them that the subway system was rife with “security breaches, mismanagement, corruption scandals, and missing money.”

Mr. Casale said subway tunnels such as the one beneath the East River at 63rd Street represent the most vulnerable assets in the system. If a terrorist bomb breached the tunnel, the river could flood the connecting tunnels with millions of gallons of water. Mr. Casale cited one study that said 19,000 people could be killed in a scenario that would paralyze the transit system, and the economic activity it generates, for years.

“You cannot stop the East River,” Mr. Casale told The New York Sun. “You can’t send a diver down with a cork.”

A 20-year police veteran, Mr. Casale worked for the MTA from January 2002 until May 2003, when he and his boss, Louis Anemone, were fired for reasons unrelated to security. Mr. Casale allegedly fabricated the existence of a confidential informant in connection with a corruption investigation he initiated. This spring, a judge in state Supreme Court ordered that Mr. Casale be given what is called a “name clearing” hearing.

Mr. Casale said the $591 million allotted to the MTA for security should be handed over to the city’s police and fire departments, whose counterterrorism units, he said, are better equipped to secure the transit system. He also asked that the state comptroller, Alan Hevesi, oversee how the security money is spent.

A Hevesi spokesman, David Neustadt, said: “Serious issues have been raised, and we are considering the appropriate response.”

In the aftermath of last week’s London bombings, Mr. Casale also told reporters of negotiations he initiated with the Army to develop technology to secure the tunnels with sensors, infrared cameras, and floodgates, as well as other security measures. In October 2003, those consultations ended when the MTA said it could not agree to the Army’s conditions, including posting construction money up front and relinquishing control when service disruptions could take place in the subway, according to an MTA spokesman. The spokesman, Brian Dolan, condemned Mr. Casale yesterday for “fear-mongering” and “scare tactics.”

Mr. Dolan said that by the end of this year $358 million will have been spent on construction projects to secure “critical infrastructure” in the subway system, including tunnels under the river.

That the MTA has had delays in implementing security reforms did not surprise security consultants, who said interagency turf wars were bound to break out over an issue like security that requires cooperation.

“It appears to me that we’re having what really amounts to a bureaucratic muddle,” a senior vice president and chief operating officer of Aggleton and Associates, a security consulting firm, said.

He added, however, that in his view the MTA remains the best agency to spearhead the security of the transit system.

Since the deadly bus and subway bombings in London last week, transit security has assumed greater urgency, and legislators have acted in recent days to increase funds for protective measures. The Senate passed a bill Tuesday night to double funds from the Department of Homeland Security for high-risk areas such as New York.