The one system that gun-rights and gun-control advocates both agree on, the National Instant Criminal Background Check System, which is supposed to keep guns out of the hands of dangerous people, is riddled with problems.

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His family called him unstable and violent, so John Houser was ordered by a judge to be taken against his will to a mental hospital in 2008. Despite that sign that Houser was mentally troubled, he passed a background check and was able to legally purchase the gun he used last week to kill two people in a Louisiana movie theater, because that hospital stay was not defined by officials as an involuntary commitment.

Dylann Roof, who is charged with shooting nine people to death in a Charleston, S.C., church last month, was also able to buy the gun he used in the massacre. He should have failed a background check, federal officials said, because he had previously admitted to illegal drug possession. Yet because of a clerical error in South Carolina and the confusion that caused the federal authorities who examined his record, he was not stopped from making his purchase.

As these two cases show, the one system that gun-rights and gun-control advocates both agree on, the National Instant Criminal Background Check System, which is supposed to keep guns out of the hands of dangerous people, is riddled with problems. While the system, in operation since 1998, has prevented more than 2.4 million sales, it still has major gaps, with spotty cooperation from the states and a narrow definition of who is considered too mentally ill to own a gun.

“It works tremendously well when it’s given the tools to work,” said Dan Gross, president of the Brady Campaign to Prevent Gun Violence, an advocacy group. “But it’s widely inconsistent from state to state.”

The National Rifle Association (NRA), which declined to comment for this article, has argued that the background-check system, and the database of prohibited gun buyers, should be repaired before any other controls are considered. Gun-control advocates say that ignores the biggest flaw of all in the system, that about 40 percent of all gun sales are exempt from background checks because the seller is a private party, often operating online or at a gun show.

Federally licensed gun dealers are required to conduct a background check before each gun purchase, but private sellers are not.

Under federal law, the list of prohibited buyers is supposed to include people convicted of felonies and certain misdemeanors, drug abusers and those convicted of certain drug crimes, and anyone whom a court has involuntarily committed for being dangerously mentally ill.

But there is no requirement that the states participate in adding names to the database. Putting the states’ convicted criminals on the list of prohibited buyers generally works fairly smoothly, but the systems for adding people with drug problems have been erratic, and those for the mentally ill even more so, experts say.

Some states have highly automated record-keeping, while others have more room for human error and some still work with paper records; some scour old cases for names to add, but most do not bother; and the states use varying standards for committing people to mental hospitals against their will.

Some states have put hundreds of thousands of people with involuntary commitments on the list over the years, but in other states, the figure is in the single digits, according to records kept by both the National Shooting Sports Foundation, the trade association for the gun industry, and gun-control advocates.

On Sunday, Gov. Bobby Jindal of Louisiana argued that if Houser had been involuntarily committed in his state, he could not have passed a background check. That is because of a law the governor signed last year, requiring the state’s courts to report such rulings to the federal database. Jindal urged other states to strengthen their laws and make sure such information is reported to the federal government.

“Absolutely, in this instance, this man never should have been able to buy a gun,” he said on the CBS program “Face the Nation.”

But until that 2014 law was signed, Louisiana was far behind most states, adding just four names of mentally ill people to the prohibited-buyer list through 2013. Like several other states, it had contended that privacy laws prevented its courts from passing on the names of people committed to mental hospitals.

“States really don’t need to pass laws to send these names to the federal database, and a lot of states just go ahead and do it, but a lot of them think they do need these laws,” said Josh Horwitz, executive director of the Coalition to Stop Gun Violence, an advocacy group.

Other states have complained about the cost of keeping up the records, and even states with policies of sharing the names with the federal database vary widely in how aggressively they do so. Georgia has reported fewer than 9,000 people over the years; Virginia, with a smaller population, has reported more than 231,000.

The 2007 massacre at Virginia Tech, where a student killed 32 others and then himself, prompted a push to put involuntarily committed people on the list, and the federal government provided the states with some additional money for the effort.

The results gave some indication of how much was missing. From 2006 to 2014, the total number of prohibited buyers in the federal database tripled, to 12.9 million. The number who were put there for mental illness increased more than 12-fold, to nearly 3.8 million.

In 2008, Houser’s family asked a court in Georgia to commit him, and a Probate Court judge, Betty Cason, had him detained and sent to a mental hospital, which released him after a week. But that was not an involuntary commitment for treatment, which would have required that the court report him to the Georgia Bureau of Investigation, which, in turn, would have reported him to the federal government, Cason said Monday.

Sherry Lang, a spokeswoman for the Georgia bureau, agreed that “there was not an involuntary commitment done on him.”

An involuntary commitment would have required going back to court and obtaining a formal ruling that he should be held longer, because he posed a risk to himself or others. Most of the records, as is typical in such cases, were sealed, so it remains unclear whether the state or his doctors sought such a ruling.

The federal rules interpreting the gun law specifically say that temporary detention for evaluation does not count as commitment, and does not bar someone from buying a gun. Neither does checking into a mental hospital voluntarily. Gun-control advocates call that a loophole that allows people who are mentally unstable to buy a gun because they have never gone through the court system.

Houser bought his .40-caliber semiautomatic handgun at a pawnshop last year, and used it to kill two people watching a movie and wound nine others, before taking his own life.

Roof, who was captured after the Charleston shooting, was able to buy a gun because of sloppy record-keeping, officials say — another problem in the background check system. He was arrested Feb. 28 in Columbia, S.C., and law-enforcement officials said that he admitted illegal drug possession to a police officer, which should have barred him from buying a gun.

Experts say state and local authorities vary widely in whether they bother to add a drug offender to the federal database without a conviction. Even if they do, there is often a delay.

When Roof went to buy a gun in April, and a background check was requested, the FBI examiner who handled the request saw that he had a recent arrest, and tried to get the police report. But a jail clerk had attributed the arrest to the wrong police force, so the FBI examiner called the wrong agency, and never obtained the report.

If, after three business days, the FBI has not given an answer to a background query, a gun dealer is free to make the sale. Roof walked out of the store with the semiautomatic pistol he would take to the church in Charleston two months later.