VIRGIN Blue has sacked a male flight attendant and offered an angry mother free flights after her toddler was put in an overhead locker.

Natalie Williamson claims she, her 17-month-old son, Riley, and her now estranged husband were on a Virgin flight from Fiji to Sydney, when the flight attendant picked up Riley, placed him in the locker and closed the latch.

Virgin has admitted an incident did take place, but claims Ms Williamson's husband was playing a peek-a-boo game with Riley involving the overhead compartment when the flight attendant joined in.

"We conducted a thorough investigation of the incident and the staff member involved was subsequently terminated," a Virgin spokeswoman said.

The airline offered Ms Williamson three free flights, but the mother has said she is too shaken by the mid-air experience to redeem them.

"My husband, Shayne, was standing one metre behind my son, Riley, when the air steward picked him up and placed him in the overhead compartment," she said.

"I stood up and there were people laughing and then I said 'Get my son out of there now'," she told the Sunday Herald Sun.

"I was devastated. I was absolutely devastated.

"I was crying. My husband was in shock. For days on end I was crying."

Ms Williamson said Riley was locked in the compartment for up to 10 seconds in complete darkness.

"The manager on board came up to me later and said: 'I need you to complain, I need you to do something. Write or ring. Do whatever you can'," she said.

Ms Williamson said Riley, now 20 months, had seen various specialists since the incident after suffering from anxiety and withdrawal.

"He won't leave my sight now. He sleeps with me. If I'm not in the same room as him, he will scream and yell 'Mum, mum, mum'," she said.

Virgin said they took the incident seriously and had dismissed the flight attendant.

"The safety of our guests is our top priority and we do not tolerate any breaches of this," a spokeswoman said.

"We have expressed our sincere apologies to the guest and have provided them with a credit for the full amount of the two return flights."