The city’s police department is failing to properly organize and monitor the firearms in its custody, an audit by the city comptroller shows.

William Thompson Jr. called the findings, released yesterday, “disappointing and disturbing.”

“It’s disgraceful that the NYPD has let its weapons go AWOL,” he said at a press conference yesterday. “We found a stunning lack of organization, order, and control.”

City auditors requesting access to firearms stored by the police department’s Manhattan Property Clerk Division found that 94 of the 324 weapons they asked to see could not be immediately accounted for or retrieved, some 29% of the sample group. In some cases, the auditors reported that they had to make several trips before the firearms were found.

“When the firearms were found, they miraculously turned up in the exact same spot on the shelf where they had clearly been previously missing,” Mr. Thompson said. “Our review found logbooks with words and numbers crossed out and even papers stapled onto the pages. With this kind of outdated system, it’s little wonder why it has been a dysfunctional process.”

The audit found that regulations requiring that firearms be disposed of after a year in police custody were often ignored. Thirty percent of the weapons auditors examined were overdue for removal by the department. In one case, a shotgun and ammunition were found in storage nearly a decade after they was first entered into the system. In addition, guns were often stacked on top of each other in piles, making organization difficult.

Police officials indicated they would implement most of the report’s recommendations, Mr. Thompson said, among them conducting a new inventory of all firearms in the Manhattan Property Clerk Division’s possession, reorganizing rifles to be shelved in chronological order, and computerizing the record-keeping process.