The findings were forwarded to the U.S. Attorney's Office, which launched an investigation that is continuing.
The FBI raided the Sheriff's Office in August, saying agents were looking for evidence related to the sheriff's real estate functions.
Federal authorities also have convicted eight people in an unrelated scam within the office.
In the wake of the Butkovitz investigation, the Sheriff's Office and the Nutter administration signed a series of "memorandums of understanding" in 2011 and 2012 to set up better financial controls.
Monday's audit said millions of dollars that flow through the Sheriff's Office remain "highly susceptible to misuse" because of a lack of city oversight.
Deputy Mayor Everett Gillison said he "disagreed with the characterizations" in the Butkovitz report.
"But he's obviously doing what he has to do, for whatever his motivations are," Gillison said.
Gillison said he has worked with Sheriff Jewell Williams, who was elected after the 2011 investigation, to change operations, hire more deputies, and put in a new computer system.
"All of these things are going on at the same time," Gillison said. "They can't all, quite frankly, be done overnight. We decided, as long as we're working together, I don't mind giving him some time to get his house in order."
The latest audit showed that Williams has been awarding contracts without legal approvals, some to political contributors and friends.
Williams' office said last week that many of the contracts were for less than $32,000, below the threshold to require city approval. The agreements with the administration, however, called for approval for all contracts. Gillison on Monday reiterated his "firm commitment" to making that happen.