New York City Police Commissioner Raymond Kelly warned Wednesday that putting Khalid Sheikh Mohammed and four other suspects on trial for terrorism in New York would place an unbearable financial and security burden on a city whose policing resources were already badly stretched.

Commissioner Kelly did not openly urge President Obama to reconsider his Justice Department’s decision, saying such policy issues were Mayor Michael Bloomberg’s domain. But he saw no reason, he said, why such high-profile trials should not be held at a military base or another venue that would be less “disruptive” and pose less of a security challenge to New York. Kelly made his remarks at the annual breakfast meeting of the Police Foundation, which raises millions of dollars each year from individuals and New York-based companies to finance some of the NYPD’s more innovative counterterrorism and other programs.

Commissioner Kelly said that the Obama administration’s decision to try the five highest-profile accused terrorists in New York was not only “certain to raise the threat level” in a city that has always been al-Qaida’s top target, but would also break the department’s budget absent substantial federal assistance from Washington. “We simply cannot go forward” with the enhanced security measures his department has planned “without cash on the barrel head,” Kelly noted. Earlier this week, NYPD officials had discussed the amount of federal assistance the city would receive with President Obama’s Office of Management and Budget, but a figure has not been agreed upon.

City officials and New York Senator Charles Schumer have already urged the federal government to foot the entire security bill for the trials it recently decided to hold in New York’s criminal courts. But even if the city were reimbursed for every dollar it spent, Kelly claimed, further “erosion” in the police department’s ranks had to be expected. The department will have 34,500 officers by the middle of next year, or 6,000 fewer than it did the year before the 9/11 attacks, he said.

Kelly also outlined the elaborate, two-tiered security plan that his department would implement once Mohammed, the self-professed mastermind of the 9/11 attacks, and the four other suspects now being held at Guantanamo Bay were transferred to the Manhattan Correctional Center in downtown Manhattan. No date for the transfers has been disclosed, and Kelly said he did not know when the trial would start or how long it was likely to go on. Similar trials have typically lasted between two and three years.

He reiterated Mayor Bloomberg’s estimate that the trial would cost at least $215 million for the first year and $200 million for each subsequent year, mainly in overtime for extra NYPD patrols. Initially, the commissioner had estimated that the trials would cost the department about $75 million. But that projection rose dramatically after the NYPD conducted an analysis and devised its enhanced security plan. (Dean Boyd, a Department of Justice spokesman, wrote me in an email: “The Attorney General has stated previously that the 9/11 attacks were attacks of national consequence and national responsibility, and that, although the 9/11 trial will be hosted in New York, New York should not bear the burden of the costs associated with this case alone.”)

The measures Kelly outlined Wednesday morning foresee the creation of a two-tiered security zone and the deployment of several thousand officers in a display of force around the court complex, which includes the Manhattan Correctional Center, connected with the courthouse by a tunnel. The tunnel was a key factor in the selection of New York as the trial venue, Kelly explained, since it enabled the accused to be brought to the courthouse each day without passing through city streets. The complex, however, is only blocks away from the site of the World Trade Center.

Kelly said the department planned to establish a “soft” perimeter extending from Broadway to the Bowery and north to Houston Street, and a smaller “hard” zone immediately surrounding the federal and state court houses, the M.C.C., NYPD headquarters, St. Andrew’s Church, and the Chatham Towers, a mixed-use high-rise near the court house. The area will be under surveillance by officers in mobile towers that hover 20 feet above ground and provide a 360-degree view of the area. Sniper teams on rooftops and bomb-sniffing dogs will patrol the zones. NYPD helicopters will hover above lower Manhattan and amphibious units will monitor the East River and the Hudson to prevent Islamic militants from staging the type of raid they conducted in Mumbai. The NYPD will increase its radiation sweeps to detect the presence of a dirty bomb. Private cars will be banned in much of the hard zone and will be spot-checked within the larger soft zone.

Commissioner Kelly said that he and other city officials had made clear to Attorney General Eric Holder that the NYPD was “understaffed” for such a mission and could not afford to pay for the added security. But he stressed that neither he nor Mayor Bloomberg had been consulted about the decision in advance. Both he and the mayor, Kelly said, learned of the decision on the day it was announced.

The Obama administration’s decision to hold the trial in a civilian federal criminal court and not in a military commission has been, of course, intensely controversial. Writing in National Review Online in December, Andrew McCarthy, a former federal prosecutor who argued the terror case against Sheikh Omar Abdel Rahman for the 1993 World Trade Center attack, and Representative Michele Bachmann, a Republican House member from Minnesota, argued that the administration couldn’t justify its decision to grant a criminal trial to Mohammed and the other plotters of the “deadliest act of war ever committed on U.S. soil.” Urging President Obama to reconsider his decision to give the plotters “the same constitutional rights enjoyed by the nearly 3,000 U.S. citizens they massacred on 9/11,” they urged Congress to reverse what they called the administration’s “reckless” decision to jeopardize intelligence sources and methods and upend American criminal justice, which, since the Revolutionary War, has tried wartime enemies before military commissions rather than treating them merely as criminal defendants.

But Attorney General Holder and President Obama are apparently adamant that the trials should be held in the civilian court system, and in Federal Court, in New York. Kelly said that yet another high-profile al-Qaida figure being held at the Guantanamo Bay naval prison may be brought to trial in federal court in Brooklyn, posing an even heavier security burden on New York.

Despite having 6,000 fewer police officers than the department had in 2001, Kelly said, crime had continued dropping in New York for an eighth straight year. Serious crime, except for felonious assault, had declined by 11 percent in 2009 from its 2008 levels, and had fallen by 35 percent since 2001. Subway crime was down 13 percent from 2008. There were 2,240 murders in New York in 1990; some 466 murders were committed in the city in 2009, though New York City was home to 2.2 million more people.

Terrorism threats to the city continue, however: Kelly said that law enforcement had disrupted at least 10 plots against New York targets since 2001. Homegrown terrorism, police say, is the one security threat to the city that seems destined to rise.

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