NORTH BILLERICA, Mass. — Pan Am Railways Inc. intends to appeal a U.S. Department of Labor decision that the rail company violated the whistleblower rights of one of its Waterville employees, according to a Pan Am executive.

On Tuesday, the department’s Occupational Safety and Health Administration ordered Pan Am Railways to pay $50,000 in compensatory and punitive damages to an injured worker. OSHA said in its release that Pan Am retaliated against the employee and accused him of lying when he filed a Federal Railroad Safety Act complaint.

Pan Am Executive Vice President Cynthia Scarano said on Wednesday that there were discrepancies in the employee’s report to OSHA from his hearing with the railroad company.

The employee, who currently works in a railyard in Waterville, filed a complaint with OSHA on Dec. 6, 2011, claiming that Pan Am had subjected him to disciplinary action for reporting an injury and unsafe working conditions, according to a statement released on Tuesday by OSHA. The Department of Labor does not release names of employees involved in whistleblower complaints.

After the filing on Dec. 6, 2011, a second disciplinary hearing was held on Jan. 4, 2012, where Pan Am Railways alleged the employee made false statements to OSHA and the railroad.

Scarano said after the incident on the railroad there was a hearing conducted by the railroad and disciplinary action was taken against the employee for the incident. She declined to comment on the incident itself.

After the first hearing, the employee then filed a complaint with OSHA stating that the discipline was a retaliation against him, said Scarano. The railroad then held a second hearing.

“Upon receiving that complaint, we felt as though the two testimonies conflicted,” she said. “We had another hearing to establish the testimony, but no action was taken after that hearing. OSHA’s decision is in response to our second hearing, not our first hearing.”

Scarano explained that, under the Railway Labor Act, the railroad must have a hearing to establish the facts of an incident or accident. The first hearing was testimony from the employee while the complaint submitted to OSHA was written by the employee’s attorney, she said.

A second hearing was held to clear up the discrepancies, she said.

“OSHA found that the employee engaged in protected activity when filing the complaint, and the railroad took retaliatory action by charging him with lying and by holding the second disciplinary hearing,” OSHA said in a statement released on Tuesday. “Such adverse action can intimidate employees from exercising their FRSA rights, even if the charge is later dropped, as it was in this case.”

“Employers must understand that their employees have a legal right to file a whistleblower complaint with OSHA without fear of retaliation,” said Marthe Kent, OSHA’s New England regional administrator. “Responding to an employee’s complaint with threats of disciplinary action is not acceptable and prohibited by law.”

Pan Am Railways was also ordered to take corrective action, OSHA said. It must expunge all files and computerized data systems of disciplinary actions and references to the hearing notice and January trial. Pan Am must also post notices about its FRSA whistleblower rights at all its Maine locations and internal website.

OSHA also ordered Pan Am to pay reasonable attorney’s fees and compensate the employee for wages and benefits lost due to attending the January disciplinary hearing, according to the release.

A timeline of when the appeal will be filed and how long the process could take was unknown, said Scarano.

The rail company stresses safety, she said.

“Safety is the No. 1 priority with our railroad,” Scarano said. “We take it very seriously.”