A Virgin spokesperson told news.com.au in a statement that "Virgin Australia flights to Denpasar will temporarily be required to make a short stop to re-fuel in Darwin".
"Passengers will not be required to disembark, and the stop will take approximately 30 minutes," the statement reads.
"The difference to overall flight time will be an hour, and we are moving departure times forward to ensure flights land on time."
Virgin added the stopover was due to maintenance works and wouldn't be a permanent measure.
"This is due to maintenance works and changes to operating hours at airports within the region during the pandemic, we are currently required to carry more fuel than we ordinarily would (to get to alternate airports if required)," the statement continued.
"We had a choice to reduce the number of passengers we would carry on our flights to conserve fuel, or to make a stopover in Darwin to re-fuel and have everyone who had booked arrive in Bali on schedule.
"To make sure everyone gets to Bali, we chose to re-fuel."
Meanwhile, Virgin Australia has also announced it will roll out direct, daily flights from the Gold Coast to Bali in March 2023.
The flight will take about six and a half hours, with 2200 seats per week flying between the popular holiday destinations.
Seats are available to book now, with travellers planning for next year currently able to secure return tickets for just over A$500.
Competitor Jetstar has also announced a major flight sale, which includes flights to Bali for just over A$100.