Australia's Fair Work Ombudsman (FWO) is suing Jetstar over claims it contravened workplace laws when it hired the trainee pilots.
The work the pilots performed was exclusively in Australia but the airline erroneously told them their employment was governed by New Zealand laws, not Australian laws, during the training period, according to the Ombudsman.
It alleges Qantas-owned Jetstar sought to have the six New Zealanders hired pay the cost of their own training despite this being prohibited under the Australian Air Pilots Award.
The pilots reimbursed Jetstar A$17,500 between June and September 2011 before the practice ceased.
Jetstar refunded the money in November 2011 as a "goodwill gesture".
The Ombudsman also alleged Jetstar didn't pay the trainees superannuation, a requirement under Australian employment law, during their training period.
"Multinational companies with wholly or partly-owned overseas enterprises need to exercise caution and care if they engage workers under those entities and then have them work in Australia,'' Ombudsman Nicholas Wilson said.
The maximum penalty faced by Jetstar and its New Zealand subsidiary is A$33,000 per breach.
Jetstar has said it will defend the claims and has already paid cadets any shortfall between New Zealand and Australian superannuation as a gesture of goodwill.