JetBlue flight 1002 from Fort Lauderdale, Florida, to New York's John F. Kennedy International Airport was originally supposed to depart at 1:42 p.m. ET, but six delays pushed the departure time to just after 8:00 p.m.
Once the plane boarded, the pilots informed passengers that 10 of them needed to move from the front to the back of the plane due to weight distribution.
Passenger Layla Delarmelina said six passengers refused and "the captain wasn't doing anything."
Delarmelina said the former senator got up and confronted the people that refused, and then told the captain to just pick people to move.
"He called them idiots and said, 'The captain needs to grow some balls,'" said Delarmelina. "So they kicked him off the plane."
JetBlue spokesman Morgan Johnston told CNN, "The decision to remove a customer from a flight is not taken lightly. If a customer is causing a conflict on the aircraft, it is standard procedure to ask the customer to deplane, especially if the crew feels the situation runs a risk of escalation in-flight."
After being told to deplane, video taken by passenger Jacqueline Galante shows D'Amato attempting to rally passengers to stand up and deplane with him.
"Stand up for what's right and walk out with me," D'Amato said. "If you don't, then what do you stand up for?"
D'Amato was then escorted from the plane by Broward County Sheriff's officers. The Sheriff Office referred comment to JetBlue, saying, "it's not a law enforcement issue."
A passenger is seen leaving with D'Amato. Galante confirmed the Republican senator did not get back on the flight.
"Anyone who knows Senator D'Amato knows he speaks his mind -- but in this case, he spoke after a long and demanding trip to Florida to visit an ailing friend," Park Strategies, D'Amato's policy consulting firm, told CNN.
The firm said JetBlue apologized to D'Amato for "overreacting" and that the former senator apologized for "speaking his mind at a time when he clearly had left his patience at the gate."
JetBlue would not confirm any apologies were exchanged.
Passengers on the delayed flight received a $200 voucher for future flights on JetBlue.
D'Amato served in the Senate from 1981-99. The New York Republican was ousted in 1998 by Democrat Chuck Schumer, now the Senate minority leader.