In a 2009 e-mail discovered by the Senate investigators, one department official warned that the fusion centers were collecting information on Americans “without proper vetting,” and were “improperly reporting this information through homeland information reporting channels.”

More broadly, the flaws uncovered by the Senate’s Permanent Subcommittee on Investigations raise questions about the role of the Department of Homeland Security in the nation’s fight against terrorism, and whether the department can ever live up to its original purpose of “connecting the dots” to prevent another surprise like the Sept. 11 attacks.

The report on the dysfunctional nature of the fusion centers makes clear that in the decade since the department was created, Homeland Security has not carved out a clear counterterror mission that does not overlap with those of other agencies.

Top officials of the Homeland Security Department have known about the problems for years, but hid an internal department report on the program’s flaws from Congress while continuing to tell lawmakers and the public that the fusion centers were highly valuable and that they formed the centerpiece of Homeland Security’s counter-terrorism efforts. A 2010 internal assessment by the department discovered, for instance, that four of its claimed 72 fusion centers did not exist, even as department officials kept using the 72 figure publicly with Congress.

Homeland Security officials disputed the findings of the Senate investigators. Matthew Chandler, a department spokesman, said the Senate report “is out of date, inaccurate and misleading.” He said the investigators “refused to review relevant data, including important intelligence information pertinent to their findings.”

When it was created, the Department of Homeland Security was supposed to function as a central clearinghouse for terrorism-related intelligence, to solve what was supposed to be one of the big problems identified in the government’s failure to prevent 9/11 — a lack of intelligence sharing between the F.B.I., the Central Intelligence Agency and other agencies.

But almost immediately, the George W. Bush administration created other organizations to do much the same thing. Today, the central clearinghouse is the National Counterterrorism Center, part of the Office of the Director of National Intelligence.