The civil liberties group released department data that showed officers had made 123,000 citizen stops last year, resulting in 494 searches and yielding nine guns and one knife.
Police could not provide any audits or memos regarding oversight of "stop and frisk" searches, and the American Civil Liberties Union of Maryland said the data was so implausible that it "suggests a lack of supervision and accountability."
In a statement issued Wednesday afternoon, Batts said the group is right.
Batts, who took over the department in September 2012, said he has "long-standing concerns regarding the data collection methods employed by the BPD."
"This has been an issue for more than half a decade and is a pressing concern for the agency," the statement said. "The BPD is required to maintain these records for good reason, and since the arrival of Commissioner Batts long-needed reforms are being instituted throughout the organization."
The statement said Batts had asked the ACLU as well as the NAACP "to be active partners in helping move the Baltimore Police Department forward."
A department spokesman did not respond to a request for further comment.
Sonia Kumar, a staff attorney for the ACLU, said she was encouraged by Batts' remarks and awaits "concrete and immediate steps" to improve the department's accountability. The ACLU has asked for documents related to the stops, but the department said it would cost thousands of dollars to provide them.
"From our perspective we think a critical step in the right direction is for the department to provide the records we requested so that we can conduct an independent analysis," Kumar said.
The agency's officers are required to document many interactions on "citizen contact" forms. Those include vehicle stops, "involuntary detentions not resulting in arrest," and all stop-and-frisks.
Additionally, state law requires police to report each "stop and frisk" interaction to Maryland State Police.
For years, the department has reported low numbers of such stops. A review in 2005 suggested that police had conducted thousands, possibly tens of thousands, of citizen stops but had reported just 11 to the state.
At the time, then-Mayor Martin O'Malley called for improved record-keeping and training to better monitor stop-and-frisk, saying he supported the "legal and constitutional use of this tactic" but that police had to improve the accuracy of its statistics.
In recent years, the agency has reported about 220 stop-and-frisks per year — still less than one stop-and-frisk across the city per day.
Data released to the ACLU under a Public Information Act request said police had stopped 59,000 people in 2010, only 203 of which were searches and recovering guns or drugs in just 34 occasions. In 2011, 209 searches resulted from 80,000 stops, leading to the recovery of drugs and weapons 12 times.
For 2012, the agency said, its officers had made 123,000 stops but had entered only 90,000 of them into databases for analysis. Of those, officers had searched people 494 times and found drugs, guns or weapons 20 times.
Baltimore Deputy Commissioner Jerry Rodriguez has said police here don't use the tactic the way police do in New York, and moved to change the name to the broader term "investigative stops."