This story was updated at 10:15 p.m. with comments from the officers' union.

About a third of the police officers assigned to the PATH rail system are facing disciplinary action after an internal inspection revealed they had spent hours, sometimes almost entire shifts, in break areas instead of on patrol, the Port Authority of New York and New Jersey said Wednesday.

The agency is also weighing whether some of the 44 cases should be referred to local prosecutors.

The officers' union said, however, that the investigation started only after the union filed a civil rights lawsuit in New York alleging officers' cell phones were searched illegally. Port Authority officials, including the lead investigator who found officers were failing to staff their posts, are defendants in that suit.

"The allegations against these officers are extremely serious and we believe they have let down the public they are sworn to serve,'' said Port Authority Inspector General Michael Nestor. "We will seek to take significant action against those officers who violated the public trust."

But Bobby Egbert, a spokesman for the Port Authority Police Benevolent Association, blasted the agency for "issuing a press release" regarding "internal disciplinary matters."

Egbert also touted the low rate of crime at PATH facilities as proof the agency's officers were doing their jobs.

"The PATH system consists of four lines covering nearly 14 miles of track with 10 stations in two states. The PATH system served more than 50 million passengers in 2016. Despite riding through the densely populated urban environments, the entire system had 15 reported robberies in 2016. Eight of those robberies were closed out by arrest by a responding officer on the scene. The PAPD is doing its job to keep our patrons safe, contrary to the Port Authority's attacks," Egbert wrote.

In May, the Quality Assurance and Inspections Unit of the Chief Security Officer noticed several officers were not at their posts during a routine inspection of the region's 13 PATH rail stations. PATH lines run between Newark, Harrison, Jersey City and Hoboken as well as lower and midtown Manhattan.

An investigation was launched by the Office of the Inspector General beginning at the Hoboken station but eventually spreading to other stations in both states, including 33rd Street, the World Trade Center, Newark Penn Station and Christopher Street. Investigators learned that officers, mostly working the midnight to 8 shift, were spending more than six hours in break rooms, with one officer spending the bulk of his shift, seven hours, away from his post.

Some of the officers who allegedly skipped the patrols also include personnel pulling overtime in response to terrorist attacks in the U.S. and internationally.

The allegations are supported with video evidence, the agency said.

Egbert, however, said the agency does not specify an appropriate amount of time officers should spend in what he described as "emergency rooms," which he said are part of an officer's post and from where officers can monitor the area via surveillance camera. In addition to breaks, Egbert said the rooms are also used to prepare reports and also contain emergency equipment.

The officers, whose names were not disclosed, all remain on duty at normal pay, said Scott Ladd, an agency spokesman. Under the terms of their contract officers cannot be suspended unless they're indicted, arrested or fail a drug test, Ladd also said.

The agency's top commander, Robert Terrett, was reassigned in the wake of the allegations. To date, none of the accused officers have settled the disciplinary charges and all 44 cases remain pending.

Paul Milo may be reached at pmilo@njadvancemedia.com. Follow him on Twitter@PaulMilo2. Find NJ.com on Facebook.