The report also raised questions about the justification for frisks.
Many police reports detailing a frisk claim the suspect had a "bulge" in a pocket, the report said. "Bulges" almost inevitably turn out to be cellphones or wallets, the report said.
Of 2,380 pedestrian stops detailed in the report, only six produced guns and 36 produced non-gun contraband.
The report is the sixth in a series of studies done as part of a settlement agreement between the city and the ACLU. All have found widespread violations.
The ACLU warned in the report that it would seek sanctions in federal court if "rapid and significant progress" is not made.
"We understand that Mayor Kenney's administration did not create this problem," David Rudovsky, counsel for the eight men who filed the initial class-action lawsuit in 2010, said in a statement. "But Philadelphians have waited too long for a change. 2016 is the year that the PPD needs to show that it can comply with the consent decree without the need for court-ordered sanctions."
Representatives from the administration, the ACLU, and Rudovsky's law firm met in federal court Tuesday morning to review the findings with U.S. District Judge Stewart Dalzell.
Speaking to reporters outside the courthouse, Police Commissioner Richard Ross said the department agreed with the report's assessments and had made some changes. More will come, he said.
"The bottom line is, the truth will be in the numbers coming forward," Ross said.
Commanders will be responsible to answer for pedestrian stops, he said. In addition, Ross said that captains will audit reports on stop-and-frisk stops on a daily basis instead of monthly, and officers will get improved training in filing reports detailing stops. Officers who consistently make bad stops will face disciplinary action, Ross said.
Kenney campaigned on ending stop-and-frisk but has said since that he wants to make sure its use is constitutional and limited.
Ross said Tuesday that Kenney had rightfully "modified" his position.
"It is a law enforcement tool that arises out of a federal-court case from many, many years ago," Ross said, "and if you were to take that away from police officers, you would have chaos on the streets of this nation. What is imperative is that you do it constitutionally."
As for the disproportionate number of minority stops, Ross said the large number mirrored the large number of minority victims.
"The level of victimization in this city is at least that much in neighborhoods of color, if not higher," he said. "That is a fact that you cannot deny, and when people talk about neighborhoods being over-policed - well, where would you suggest we have them?"
While Rudovsky said he was cautiously optimistic the city's performance can improve, he had expected more progress by now.
"To be fair, when we started this process, we did expect it would take some time," he said. "We're dealing with a huge police force, cultural issues, management issues. But I don't think anyone expected four to five years."