TRENTON -- The U.S. Department of Labor is investigating NJ Transit for widespread abuse of the federal Family Medical Leave Act, NJ Advance Media has learned.

Alleged abuses by rail and bus operations employees have resulted in "delays and cancellations of service due to unavailability of rail crews, bus operations and light rail operators," "higher costs" from overtime paid to their replacements and compromised safety due to "delay in making mechanical and signal repairs," according to an an internal audit conducted in May and obtained by NJ Advance Media.

The audit found a history of NJ Transit employees who "call-out to use FMLA time just before their shift is scheduled to begin, or even it has begun." The practice has left managers with "gaps in operational coverage" that incur additional overtime costs for NJ Transit, according to the audit.

Additionally, a memo written a month later to NJ Transit's executive director Steve Santoro by former chief compliance officer Todd Barretta warned that NJ Transit's deficiencies are not just related to FMLA compliance, but rather represented "an overall poor corporate culture that permeates and plagues our organization."

"It's an agency out of control and it needs to be turned around, immediately," said Assemblyman John McKeon, D-Essex, co-chair of a joint legislative oversight committee that has been investigating NJ Transit since a derailment at New York's Penn Station last April.

In his June 2 memo, Barretta warned that "NJT's leniency results in an off the charts rate of employees approved for FMLA" and that the agency's "weaknesses have fostered a culture of FMLA abuse."

Some 1,500 NJ Transit's employees were approved for unpaid family medical leave as of mid-May -- a figure representing more than 10 percent of the entire workforce at the nation's second largest railroad -- according to the May audit.

Barretta was fired as compliance officer earlier this month by NJ Transit for misusing a company car after five months at the agency.

The documents were provided by two sources who requested anonymity because they were not authorized to speak publicly about the federal investigation.

Fired NJ Transit Chief Compliance Office Todd C. Barretta testified before the Legislature about the railroads many problems on Friday, August 25th, 2017 (Credit: NJ Advance Media for NJ.com)

On Friday, Barretta testified before McKeon's committee about an agency rife with mismanagement that had put passenger safety at risk. He made no reference to the pending federal investigation.

On Monday, Gov. Chris Christie assailed Barretta as giving "false and retaliatory testimony, urged on by political hacks like (Assemblyman) John McKeon, who can't find any scandal at NJ Transit, and so they want to try to manufacture one."

On Tuesday evening, Barretta confirmed he'd warned of Santoro about "alarming" FMLA abuses, adding that they had contributed to a summer marked by numerous rail and bus service delays and cancellations.

"This is one of the major contributing causes of the manpower shortages at NJ Transit, and nobody acknowledged it until they got scared that some regulator was coming in to look at it," Barretta said.

The Family and Medical Leave Act of 1993 is a federal law requiring covered employers to provide employees with job-protected, unpaid leave for qualified medical and family reasons.

Under the FMLA, eligible employees can take up to 12 weeks of unpaid leave during any 12-month period to contend with a serious health condition of their own, or for a parent, spouse or child.

The internal report written in May by Warren Hersh, the agency's auditor general, detailed the widespread use of the FMLA for last-minute or even after-the-fact absences and called for "immediate corrective action." Hersh's audit also found the manpower shortages left NJ Transit "clearly deficient in critical ways exposing the organization to unacceptable risk levels."

Hersh's audit found that "intermittent FMLA (i.e. using FMLA time in short blocks -- a day or days, or even hours) is more prevalent at NJT than the use of consecutive FMLA time (weeks for surgical recuperation, maternity leave, etc.)"

It also noted that there "are instances where employees call out to use FMLA time just before their shift is scheduled to begin or even after it has begun...leaving managers with gaps of operational coverage."

And the report concluded that because "a high concentration" of employees taking time off via the FMLA were "in bus and rail operations" and most were using intermittent leave, the risks to NJ Transit's passengers were becoming exponential.

As NJ Advance Media reported earlier this summer, of the 112 total NJ Transit trains canceled between July 1 and July 17, only 40 were not blamed on crew shortages.

The FMLA abuse reportedly comes from unions pushing back against recently implemented policies requiring stricter attendance, according to the May audit.

"There is a direct correlation with stricter time and attendance policies and the increase in FMLA applications," wrote Hersh. "It was noted that certain unions are encouraging their members to apply for FMLA coverage due to a revised occurrence-based attendance policy."

It's not clear when the new attendance policy took effect, but Hersh wrote that after it did, bus operations saw FMLA certifications increase 400 percent -- from approximately 200 applications to 800, out of 3,500 bus operators.

On Tuesday evening, an NJ Transit spokeswoman, Lisa Torbic, declined to answer questions about the federal and state probes into NJ Transit, but did email a statement.

"NJ TRANSIT is working with the Department of Labor in its review of NJ TRANSIT's FMLA program. We welcome this review. In fact, prior to the DOL's review, Executive Director Steven Santoro asked the Auditor General to conduct an internal audit of the program based on indications it may have an impact on the delivery of our daily service. In addition, NJ TRANSIT will be implementing a technology application to improve FMLA tracking across the organization."

Calls placed to Hersh were not returned.

A Philadelphia-based regional spokeswoman for the U.S. Dept. of Labor, Lenore Uddyback-Fortson, confirmed the federal probe, but declined to comment further.

Claude Brodesser-Akner may be reached at cbrodesser@njadvancemedia.com. Follow him on Twitter @ClaudeBrodesser. Find NJ.com Politics on Facebook.