"It's disgraceful that the NYPD has not taken the necessary steps to protect New Yorkers from the very firearms that it confiscates in order to protect our city," Thompson said in a statement.
Because of sloppy paperwork and other problems, the department initially failed to produce 94 of 324 guns asked for in the audit.
The weapons eventually turned up, but only after repeated inquiries and several weeks, the report said.
The audit recommended the NYPD develop an electronic database to help keep track of all property, including guns, cash and narcotics. The department told Thompson's office that it believes its current property practices are sound, and that it is already in the process of computerizing records.
