Two years ago, detectives offered a 12-year-old boy they had arrested a McDonald’s soda during questioning. When the boy left, the detectives took the straw, got his genetic profile and put it in a local database. The child’s family had to petition a court to get it removed, the Legal Aid Society said.

For years, New York City has been amassing an immense local database of DNA, collecting samples not just from people convicted of crimes, but from people simply arrested or questioned, including minors.

The existence of the database, which has about 82,000 profiles, has drawn fire from civil liberties advocates, who point out it is hard to get a profile erased once it is put in and argue it violates the privacy rights of many innocent people.

Now, the police commissioner, Dermot F. Shea, seeking to quell some of the criticism, has announced that the New York Police Department is overhauling its rules for collecting and using DNA evidence, which is stored by New York City’s Chief Medical Examiner.

To start, the police are going to audit a database of 32,000 samples collected from people considered suspects in criminal investigations and flag for removal any samples more than two years old that have not been linked to an ongoing investigation or conviction.

Bob Barrows, the department’s director of legal operations, said that in the next few weeks he expects to remove thousands of profiles in the database, known as the Local DNA Index System, as the department begins its review.

“We don’t want to saturate the database with profiles that aren’t yielding any results,” Mr. Barrows said. “If these people are not convicted, if they are not a suspect in a law enforcement investigation or ongoing prosecution, those are profiles we want to look at.”

Public defenders and civil liberties lawyers, however, said there was no guarantee the police would expunge records as promised. Terri Rosenblatt, Supervising Attorney of the DNA Unit at The Legal Aid Society, said she is not convinced the records would be removed and urged state lawmakers to act.

“Our lawmakers should step in with real control and oversight of the N.Y.P.D. and act to ban unlawful and unregulated DNA collection,” said Ms. Rosenblatt. “All New Yorkers should reject anything less.”

The department said it is also going to streamline the process for people seeking to have their DNA removed from the index. Those who have been acquitted of crimes, for instance, would only have to provide a document showing that they were found not guilty. Before, they were required to get a court order, which is no easy task, Mr. Barrows said.

The new rules, first reported in The Wall Street Journal, also place curbs on the collection of DNA from teenagers and children. Investigators will only be able to collect DNA from juveniles in connection with felonies, sex crimes, firearm crimes or hate crimes, not misdemeanors. And they will not only have to get the consent of the minor, but they also must notify parents or guardians, who can object to it.

In the past, Mr. Barrows said, investigators were not required to obtain permission from a minor or guardian before walking away with a piece of DNA evidence.

A growing number of law enforcement agencies throughout the country — including police departments in Connecticut, California and Maryland — have amassed genetic databases that operate by their own rules, outside of state and federal guidelines, which tend to be far more strict.

Those databases have become the center of a debate over how to strike a balance between civil rights and crime-fighting, as DNA has become an increasingly common tool in investigations and prosecutions.

New York State law requires a conviction before someone’s DNA can be included in the state-operated DNA databank. But databases built by local authorities are not subject to the state rules.

Announcing the changes for obtaining and storing DNA samples, Commissioner Shea said he hopes to build trust with New Yorkers while still continuing to collect evidence in ongoing criminal investigations.

“As a Department, we have reformed policies and practices to support a system that is fair and effective while also cultivating trust with the community,” Commissioner Shea said in a statement. “These changes are common sense and incorporate feedback we have gathered without compromising the ability for officers to successfully identify criminals, build strong cases and bring justice for victims.”

But critics of the department said the changes do not go far enough. “We need basic transparency in the database,” said Donovan Richards, the chairman of the City Council committee with oversight of the police. “This is a step in the right direction, but more needs to be done.”

Mr. Richards said he wants to see one database under one set of rules, instead of two databases controlled by local and state officials.

“This idea is half-baked,” Mr. Richards said. “It still affects black and brown people disproportionately, people who have not been convicted of anything.”

But Mr. Barrows, the police department official, said the city needs its own index to solve cases faster.

“We want to keep local control of our investigations,” he said.