New York’s controversial stop-and-frisk policy, hailed by the city’s mayor and police chief as crucial in fighting crime, could boast only a 3% conviction rate between 2009 and 2012, according to a report by the state attorney general released on Thursday.

The report by Eric Schneiderman, the first detailed examination of the policy’s arrest and conviction rate, used data from the New York Police Department and the Office of Court Administration to examine approximately 2.4m stops over the three-year period. Those stops resulted in almost 150,000 arrests, but only half of those led to a conviction or a guilty plea.

Opponents of the policy, which is viewed by civil rights activists as unfairly targeting African-Americans and Hispanics, seized on the report. But the NYPD attacked it in strong terms, saying that it was meaningless because it did not make a comparison with the outcomes of arrests not carried out under the stop-and-frisk policy.

The NYPD practice, known fully as "stop, question and frisk", was ruled unconstitutional earlier this year. The administration of outgoing mayor Michael Bloomberg is appealing against the ruling, although the future of the litigation is in doubt as the newly elected mayor, Bill de Blasio, is an opponent of the policy and has pledged to replace the police chief, Ray Kelly.

Schneiderman's study found that 0.3% of the 2.4m stops led to jail sentences of more than 30 days, and 0.1% led to convictions for violent crime. It also found that there had been a “sharp uptick” in litigation costs for the city due to the cost of defending the NYPD from lawsuits.

The attorney general said the stop-and-frisk report had “broad implications for law enforcement” in New York City and across the state. “It’s our hope that this report – the first of its kind – will advance the discussion about how to fight crime without overburdening our institutions or violating equal justice under the law,” Schneiderman said in a statement accompanying the report.

“The vast amount of data we analyzed over four years should serve as a helpful guide to municipalities and law enforcement officials around the state, where stop and frisk practices are used to varying degrees.”

To make a stop, police must have reasonable suspicion that a crime is about to occur or has occurred – a standard lower than the probable cause needed to justify an arrest. The report showed that around 6% of the 2.4m stops between 2009 and 2012 led to arrests – 150,000 in total. Half of those arrests led to convictions.

Some 2% of those arrests – or 0.1% of all stops – led to a conviction for a violent crime. Only 2% of arrests led to a conviction for possession of a weapon.

“The attorney general’s report has confirmed what young men of color have known for years – that the Bloomberg administration’s stop-and-frisk crusade is targeting innocent people and is pathetically ineffective and inefficient in apprehending criminals,” said New York Civil Liberties Union executive director Donna Lieberman. “The new administration must make reforming the NYPD and its abuse of street interrogations a top priority.”

John McCarthy, the deputy commissioner of the NYPD, rejected the study. "The report is clearly flawed, which is why it makes absolutely zero recommendations," he said in an emailed statement.

"By intentionally ignoring the question of whether a stop can be an effective tool in preventing a crime before it occurs, and failing to compare SQF [stop, question and frisk] arrest outcomes against other arrests, this analysis falls short of being a meaningful review of stop, question and frisk as a law enforcement tool. "

A federal judge, Shira Scheindlin, ruled the practice unconstitutional in August. Her ruling was stayed by an appeals court in October, which declared she was biased and removed her from the case. The ruling halted a range of changes she ordered, including the appointment of an outside monitor to oversee major changes to the NYPD and reforms to police training and supervision. The appeals court refused to reconsider its ruling on Wednesday.

Bloomberg’s term as mayor will end on 31 December.