It was understood replacement parts for some aircraft had to be "road freighted" across the US, slowing the service of some aircraft.
The airline downplayed supply chain issues saying that the 787s had suffered a series of "unfortunate" events.
A spokesperson for Jetstar says the three of the aircraft were back in service by the end of the week and two more would aim to be operational by next week.
A further aircraft remains out of service, awaiting delivery of parts from the US.
"While these events were out of our control, we understand the significant impact this has had on our customers and we sincerely apologise for the frustration and inconvenience this has caused," said the airline.
"The team is working hard to return these aircraft to service as quickly as possible."
4000 travellers stuck in Bali
Since the beginning of the month the airline has cancelled eight return services between Australia and Denpasar, delaying others by as much as 24 hours.
Pre-pandemic Jetstar operated 85 return flights per week to Bali, carrying more than 2 million customers annually. Without direct flights from New Zealand, Kiwi travellers also been caught up in the disruption to budget links to Bali.
Parent company Qantas Group says it has been arranging five "special flights" to repatriate travellers from Indonesia.
Jetstar is offering Impacted customers in Bali reimbursement for accommodation of up to Au$150 per room and AU$30 per person for meals and expenses.