Alaska Airlines is under fire after a man said he and his boyfriend were told to sit apart on a California-bound plane because a straight couple wanted to sit together.

David Cooley, owner of a popular gay bar in Los Angeles, said he and his partner had been in their assigned premium seats aboard Alaska Airlines Flight 1407 at John F. Kennedy International Airport in New York when a flight attendant approached them.

His partner, Cooley said, was asked to relinquish his premium seat and move to an economy-class seat so that another couple could sit next to each other.

Cooley told the attendant that they, too, are a couple and they wanted to sit together. But still, he said, his partner was given a choice: Move to coach or get off the plane.

"We could not bear the feeling of humiliation for an entire cross-country flight and left the plane," Cooley said in a Facebook post recounting the incident. "I cannot believe that an airline in this day and age would give a straight couple preferential treatment over a gay couple and go so far as to ask us to leave."

Alaska Airlineshas since apologised and said it is investigating the incident.

"This unfortunate incident was caused by a seating error, compounded by a full flight and a crew seeking an on-time departure and nothing more than that," the airline said.

"It's our policy to keep all families together whenever possible; that didn't happen here and we are deeply sorry for the situation. We've reached out to Mr Cooley to offer our sincere apologies for what happened and we are seeking to make it right."

"Alaska Airlines has a zero-tolerance policy for discrimination of any kind," the airline added.

A spokeswoman did not immediately respond to a follow-up question about what caused the seating error, but the airline told CBS News that it had mistakenly booked two people in one seat.