A university student flushed her emotional support hamster down the toilet after airline staff told her the rodent would not be allowed on the plane.

Belen Aldecosea claims that she called Spirit Airlines twice before catching her flight from Baltimore to South Florida to confirm that she could bring her hamster, Pebbles, on the plane, reports News.com.au.

She was reportedly told that her pet would not be an issue but when she arrived to catch her flight she found out that this was not the case.

The airline refused to let Pebbles on the plane and, as Ms Aldecosea didn't have anyone to come get the rodent, a staff member allegedly suggested she either let the animal free or flush it down the toilet.

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Ms Aldecosea booked a later flight and came to the decision that flushing Pebbles would be the most humane thing to do.

"She was scared. I was scared. It was horrifying trying to put her in the toilet," Aldecosea told Miami Herald.

"I was emotional. I was crying. I sat there for a good 10 minutes crying in the stall."

Spirit Airlines have denied that any employee told Ms Aldecosea to flush her pet.