I n 2007, the New York Police Department released a lengthy report on the “homegrown” terrorist threat. The widely publicized tome sparked much controversy. The U.S. Senate’s Homeland Security Committee endorsed it, and police departments around the country continue to rely on its findings. But Muslim and civil liberties groups objected to its strong implications linking religious behavior and terrorism, and to its suggestion that New York is a hotbed of Muslim terrorism.

Now, the NYPD has issued a welcome revision of the report—very, very quietly. It added a “Statement of Clarification” that backs away from some of the report’s most troubling conclusions. New York Police Department Commissioner Raymond W. Kelly deserves credit for taking this step. But the department should do much more to clear up the misperceptions created by its handiwork.

The original study probed 10 terrorist attacks, looking to identifying behavior patterns associated with radicalization. This small sample was woefully inadequate; worse, the authors failed to consider whether these behaviors were also the norm among observant Muslims. The profile of a latter-day terrorist that emerged from the report was a Muslim man between the ages of 15 and 30, who had stopped smoking and gambling, wore traditional Islamic clothing and a beard, prayed five times a day and was involved in community activity. It goes without saying that thousands of law abiding Americans fit this description.

The report further implied that Muslims in the United States present a threat to public order. Without evidence, it claimed that violent ideologies are “proliferating…at a logarithmic rate” and that “radicalization permeat[es] New York City, especially its Muslim communities.”

Community and civil rights groups were concerned that using normal religious behavior as a proxy for terrorist tendencies would encourage religious and ethnic profiling. Such concerns were hardly imaginary. After 9/11: thousands of New Yorkers were subject to “special registration” on the basis of their ethnicity or religion, and the very act of praying before boarding a flight was considered sufficient cause for off-loading and detention. Community leaders organized and met with Mr. Kelly to put forward a critique of the report.

Happily, the recently added clarification takes account of many of their concerns. Most importantly, it disavows the original report’s linkage of religiosity and terrorism, stating unequivocally that increasing religiosity amongst Muslims “cannot be used as a signature of someone potentially becoming a terrorist.” Indeed, it concedes that law enforcement would be “wasting significant resources” if it tracked people on the basis of such behavior and cautions that the report “cannot be a license for racial, religious or ethnic profiling.”

The clarification also pulls back from the original report’s conclusion that New York’s Muslim communities have been “permeated” by radical ideologies and states directly; the New York Police Department’s “intention was never to suggest that NYC’s Muslim community has been saturated by extremism.”

So far, so good. But Mr. Kelly’s brave rethink has been undercut in two ways. For starters, the new version does not appear to have been distributed, much less publicized. The Muslim community groups had no idea that a clarification had been issued until it was mentioned at a social gathering hosted by Mayor Michael Bloomberg. At the very least, federal law enforcement agencies and other police departments should have the new version flagged for their attention.

Moreover, the changes are all crammed into a clarification, but the original and highly troubling report itself has not been fixed. Some readers will see the report as the “real” view of the NYPD and the clarification as a sop to noisy protesters. That would be a shame.

Mr. Kelly could help clear up uncertainty about the NYPD’s view by taking a few clear, bold actions. Let him both show and tell New York and the rest of the world that the NYPD does not use religious or ethnic profiling in selecting targets for terrorism investigations. Does the NYPD monitor the religious behavior of Muslim New Yorkers? If not, let the commissioner make this clear. It would be helpful too if he defined and publicized the standards by which the NYPD begins investigations and monitors Muslim religious and community spaces.

The publication of the clarification also serves as an excellent opportunity to strengthen the lines of communication that developed in response to the 2007 report. Muslim community members are critical sources of information about potential terrorist plots, and can help understand the process by which disaffected people are sometimes driven to extreme actions. Building a strong working relationship with the Muslim community may be one of the most valuable contributions the NYPD can make to our collective security.

Faiza Patel is an attorney at the Brennan Center for Justice at New York University School of Law. The Center serves as legal adviser to the Muslim American Civil Liberties Coalition.