HE horse-drawn caisson drew to a halt near Section 7 of Arlington National Cemetery. The flag was lifted from the coffin, rifles were fired and trumpets sounded "Taps." Richard Helms, the man whom the current director of Central Intelligence, George Tenet, called "the most complete American intelligence officer," was laid to rest last Wednesday. Nearby, standing in small clusters, the old guard and the new paid their respects.

The timing seemed almost fated. The day before, the intelligence establishment entered a new era as the Senate gave final approval to the new Department of Homeland Security. Rather than top-down control by the director of central intelligence, a hallmark during the Helms years at the height of the cold war, the spy world now seems likely to be further decentralized and dispersed, with the Pentagon and Homeland Security competing with the C.I.A. and the F.B.I. for the president's ear about terrorist threats.

The new department was not sold to the public that way. The idea was supposed to be that securing the homeland was one job, to be done under one roof. Now, it seems, the F.B.I. and the C.I.A. will stay largely under their own roofs, while new intelligence-handling offices will grow in the new department.

Many current and former intelligence officials worry that the department, soon to be the second largest agency in the federal government after the Pentagon, will drain experienced analysts from their existing agencies and further reduce the C.I.A.'s role as the principal agency for analyzing intelligence.

With limited financing, the department will have to staff its intelligence department with analysts not only from the C.I.A., but also from the National Security Agency, the National Imagery and Mapping Agency, the Defense Intelligence Agency — all of which report to the Defense Department — and other offices. These agencies are already stretched thin, after years of budget cutting, and losing a dozen or so important analysts could be devastating.

Others in the national security area are concerned about the growing possibility of "analysis shopping" — in which White House officials and other senior policy makers pick and choose where to go for their analyses depending on what result they want. If the C.I.A. comes up with a report not to their liking, they can then go to the Pentagon, or the Department of Homeland Security. This follows reports this fall that the Pentagon set up its own secretive intelligence unit to try to find links between Saddam Hussein and the Sept. 11 attacks after the C.I.A. concluded that none appeared to exist. "They are politicizing intelligence, no question about it," said Vincent M. Cannistraro, the C.I.A.'s former counterterrorism chief, referring to the Pentagon.

Duplication of effort is another concern. For example, the C.I.A. already has a counterterrorism center, staffed with hundreds of analysts from the various intelligence agencies, whose job it is to do analysis similar to that planned for the new department. In fact, all the intelligence agencies have counterterrorism departments. Some officials worry that the new department will simply become a redundant layer..

Critics of the reorganization have also questioned the wisdom of resorting to the same kind of office reorganization used in revamping the military in the 1940's. They say that in the 21st century, efficiency can be found by moving information rather than people. After all, a breakdown before Sept. 11, 2001, took place between two people within the same small agency: An F.B.I. agent in Phoenix, suspicious that Al Qaeda members might undertake flight training, never connected with fellow agents in Minneapolis who had arrested a suspected terrorist at a flight school.

With the intelligence bureaucracy already decentralized, this argument goes, it might be wiser to concentrate more on the wires under the floor than the wires on organizational flip charts. Rather than simply sending his memo up the F.B.I.'s slow and cumbersome chain of command, the agent in Phoenix might have simultaneously entered a copy into a computerized database shared by other agents, who then might have made a connection by simply entering a few key words, like "Al Qaeda" and "flight school."

The basic network for this system is already in place, but it is not available for use at the level of individual agents. Known as Intelink, it is the spy world's secret, secure intranet and it operates much like the public Internet. Set up in 1994, Intelink connects all of the major intelligence organizations, from the C.I.A.'s Office of Advanced Projects to the Intelligence Community Librarians' Committee.

But until now, at least, it has not been easy to fully include lower-level F.B.I. agents in such an arrangement. Not only does the F.B.I. have a famously antiquated computer system; it is primarily a law enforcement agency, whose prosecutorial interest in identifying a person's accusers could clash with a spy agency's interest in keeping sources of information secret. That is exactly the kind of problem that centralizing intelligence gathering is supposed to address.

Over lunch several years ago, Richard Helms noted that a shift in power over the intelligence community, from the C.I.A. to the Pentagon, had begun even before his tenure. It was something that worried him greatly, especially the independence of the analysis.

"Without honest, unbiased assessments," he said, "you have nothing."