NYC Ferry employees refused to allow three Muslim families to board a ferry because of a "security issue," according to a discrimination complaint filed with the New York City Commission on Human Rights on Tuesday.

The complaint, filed by the Council on American-Islamic Relations, said the families took a NYC Ferry without incident from Bay Ridge, Brooklyn, to the Wall Street stop on Sept. 21. They then decided to take another ferry to Brooklyn's Pier 6.

The families requested to board the Brooklyn-bound ferry last because they had a double stroller and many children, according to the complaint. After all the other passengers boarded, the women and their children attempted to board but were stopped by NYC Ferry employees who said there was a "security issue."

Two of the women were wearing hijabs, as well as other religious clothing, and have pronounced accents, the complaint says.

Everyone deserves equal and fair service free of discrimination, especially when using public transportation like the NYC Ferry. These families were humiliated and traumatized in public view because they happen to be Muslim.https://t.co/iE2CT0yN3b pic.twitter.com/mp0jg1MizY — CAIR National (@CAIRNational) October 16, 2019

When one of the women asked why they were not allowed to board, an NYC Ferry employee told her that security had informed him that they could not board the ferry. They were then escorted to security in full view of the other passengers.

When they arrived at security, however, the families were told by the officers that there was no issue. The complaint notes that security was confused and did not know why employees were "blaming security."

During this encounter, the children were "crying, upset and very confused," the complaint says. One of the children, a 4-year-old boy, later asked his parents why they were treated like this by the ferry staff. His parents were "heartbroken" and did not know what to tell him to comfort him, the complaint says.

NYC Ferry employees eventually told the families that they had been denied service because their children had allegedly been standing on the seats during the first ferry ride. NYC Ferry later admitted this explanation was false, the complaint states.

After approximately two hours, the families were allowed to board a ferry back to Bay Ridge, but not before experiencing "one of the worst days of their lives."

"All New Yorkers, regardless of creed, deserve equal and fair service free of discrimination, especially when using public transportation like the NYC Ferry. These families were humiliated and traumatized in public view and treated as suspect because they happen to be Muslim. That is unacceptable. We hope the city will live up to its commitment of nondiscrimination and swiftly correct this injustice," CAIR-NY Litigation Director Ahmed Mohamed said in a press release.

NYC Ferry offered to reimburse the families for their fares, calling the incident a "misunderstanding." CAIR said it is seeking payment of compensatory damages for "humiliation, embarrassment, and severe emotional distress" and punitive damages.

New York City's Economic Development Corporation, which runs NYC Ferry, told NBC News that it was aware of the complaint and is investigating the incident.

"NYCEDC takes these matters seriously, and is committed to ensuring that no person is denied services based on race, color, national origin, age, sex, religion, gender identity or disability," a spokesperson said in a statement.