More than $98,000 worth of bus fares that should have been collected during a three-year period in St. Bernard Parish are missing, according to a new audit report that casts significant doubt on explanations offered by transit officials.

The report, released Monday by the state Legislative Auditor’s Office, notes that three employees of the St. Bernard Urban Rapid Transit Department, all of whom had access to money or relevant transit records, refused to take polygraph tests in connection with the audit. All of them have denied wrongdoing, but all have either resigned or retired since the audit began.

The audit report says drivers collected $48,585 more in bus fares during the period from January 2011 to March 2014 than what ended up in the bank.

On top of that, it says, hundreds of the department’s route sheets for the same period are missing, suggesting that another $43,557 was likely collected and never deposited.

Finally, the report says, another stack of documents turned up during the audit itself, adding up to $5,963 in bus fares collected but never deposited and bringing the overall tally of missing fares to $98,105.

Passengers boarding parish buses deposit their fares in a locked box. Retrieving money from the boxes requires two different keys: one to retrieve the money from the box and another to open cabinets where the boxes are held.

The auditor’s report, which was forwarded to the U.S. Attorney’s Office in New Orleans, focuses on three transit employees who had access to the fares.

The report says that Larry Calabresi, a backup bus driver, would typically remove the fare boxes from the buses weekly, or as necessary, and bring them to a counting room in the Transit Department’s office. The report says Calabresi had keys to the fare boxes and cabinets but not to a counting room where the cash was stored.

Transportation Director Lonnie Campbell Jr. had keys to the boxes and the counting room, and Tina Pitre, the office manager, also had a key to the counting room where the cash was stored but not to the fare boxes or the cabinets, the report says.

The three employees offered various possible explanations for the discrepancies. The report says Pitre and Calabresi suggested some of the department’s paperwork may have been filled out incorrectly or that some riders may not have paid the entire fare.

Campbell blamed “longtime drivers who had been allowing frequent passengers complimentary rides” and said some drivers were only estimating rider counts, which could lead to discrepancies. At one point, he said, Pitre had “neglected a number of her job’s responsibilities.”

Pitre told auditors that Calabresi, the bus driver, had confided to her that “he changed his statements every time he talked to the auditors so he could keep them guessing,” which Calabresi denied.

In any case, all three of them denied taking the missing money but refused to undergo a polygraph exam, the report says.

It’s unclear whether criminal charges will follow the audit’s findings. Mary Beth Romig, an FBI spokeswoman in New Orleans, declined to comment on whether the agency is investigating the missing funds.

Days after his interview with auditors, Calabresi submitted his retirement paperwork, the report says. Pitre and Campbell also have since resigned their positions with the parish, Parish President David Peralta said Monday.

Peralta said internal changes have been put in place to improve accountability at the Transit Department. The changes, which largely followed recommendations made by the auditor’s staff, include making sure daily route sheets are completed by bus drivers and reconciled with deposits, and letting bank staff handle counting the fare collections.

Peralta said he began raising questions about the department’s finances after looking at budget figures and being struck with a hunch that “ridership was certainly higher than what was being documented by the amount of fares.”

The fact that all three employees have left their jobs at the department, he said, is “somewhat suspicious.”

“I must admit that I am a little bit surprised that he just up and quit,” he said of Campbell, with whom he said he had a good working relationship. “I would have to tell you that was a very unexpected and very surprising move, for as many years of service that he had with us.”