The decree took effect in 1999 and mandated procedures to stop discrimination, following an incident in 1998 when two white troopers shot into a van carrying four unarmed young men - three African Americans and one Hispanic - on the New Jersey Turnpike.
The bullets struck three of the men, who were from New York City and headed to a varsity basketball tryout at North Carolina Central University.
The New Jersey Office of Law Enforcement Professional Standards has monitored state police and studied troopers' traffic stops since the decree ended. In one of its reviews, it examined 315 traffic stops made by state police in the first half of 2012.
The comptroller's office, in its recent analysis, reviewed more than 80 traffic stops made between 2009 and 2011.
Both reports reached similar conclusions.
Black drivers are more likely to have drug-sniffing dogs search the outside of their cars than other drivers, the professional standards office said in July 2013. Despite the finding, the office said it "cannot conclude that this is the result of any bias-based practices."
It also found that some troopers failed to include all the necessary information in traffic stop files. In some cases, for example, troopers forgot to place a "consent to search" form in the file, even though the form was signed by the driver.
State Police Captain Stephen Jones said in an interview Tuesday that many of the mistakes involved the failure of troopers to check a box or to check the right box.
The professional standards office - which the comptroller's office cited numerous times in its report - said that supervisors were also "failing to identify a significant percentage of such errors." Fewer errors were missed when the professional standards office examined traffic studies in a later analysis, though.
State police responded to the findings, saying in the recent comptroller's analysis that troopers who made repeated mistakes were undergoing training more often. State police also said the continued training of supervisors in recognizing errors was needed.
"We've been making corrections every time we identify an area for improvement," Jones said in an interview.
Other parts of the comptroller's report cited malfunctions in technology used by state police on their cars, such as the audio cutting out on video recordings made by cameras. Jones said state police were in the middle of a "significant upgrade" that will improve audio quality, and hopefully prevent audio from cutting out.