The issue was believed to have been caused by a part inside the fuel pump being broken.
The captain was following standard operating procedure by turning the plane around, the spokeswoman said.
"The safety of our guests, crew and aircraft was never in question."
However, disgruntled passengers have hit out at Virgin for alleged poor communication and organisation, with one woman telling the Herald she and other travellers had been waiting at the airport for 12 hours before Virgin staff organised breakfast for them.
Staff tried to organise accommodation for the stranded passengers but a group of about 30, including the woman, missed out and were eventually told there were no rooms available, she said.
They spent the night mostly alone in the dark airport on hard, metal seats which were semi-outdoors, the passenger said, and were only offered water, after they asked for it, about 5am.
"It felt like nobody from Virgin took charge and communicated with us and the ground crew seemed in the dark as well."
The woman said they didn't hear from staff again until around 7.30am when they were called to the counter and issued with vouchers.
"These vouchers didn't cover the cost of a coffee and muffin. People were feeling upset and some very distressed by this."
At 9am Virgin Australia staff told the passengers to walk to a local hotel where they could use the facilities - like the toilet and pool - and were give $50 each to spend on food for the day, the passenger told the Herald.
"We have been awake for 30 hours. We are shattered."
She said staff notified them about 1.30pm local time, almost 12 hours after the flight landed in Rarotonga, that they would fly out at 7.15pm.
A Virgin Australia spokeswoman said staff tried their best to find accommodation for all passengers, but it was difficult to do so because of the time the plane landed.
"We apologise for any inconvenience caused to guests as a result of this change to their service."
