On 17 May 2006, the union representing Australian Qantas pilots, the
Australian and International Pilots Association (AIPA), lodged an application to the Australian industrial relations commission
Fair Work Australia, seeking to alter its eligibility rules to enable the enrolment of Jetconnect pilots in the union. On 23 May 2007 the commission ruled against the union, declining to consider the question, considering it inappropriate for the AIPA to be able to enrol New Zealand–based Jetconnect pilots, as they were already eligible to be members of the
New Zealand Air Line Pilots' Association.
In December 2009 the AIPA took Jetconnect parent Qantas to Fair Work Australia, accusing the company of deliberately driving down wages and conditions, by undermining the spirit and intent of the Australian
Fair Work Act. The AIPA accused Qantas of paying Jetconnect pilots 40 percent less than Qantas pilots, who six months earlier had been flying the majority of the airline's trans-Tasman services. Qantas was confident that it would win the case, stating: "These are New Zealand pilots operating New Zealand-originated services flying New Zealand-registered aircraft operated by a New Zealand entity".
In May 2010 Fair Work Australia president Justice
Geoffrey Giudice agreed to convene a full bench to hear the application, and in July 2010 the
Australian Council of Trade Unions (ACTU) was granted leave to intervene in the case after the ACTU argued that the outcome would have major ramifications for labour hire practice in Australia. The ACTU made its final submission regarding the case in March 2011, and in a majority decision handed down in September 2011 Fair Work Australia dismissed the AIPA's application.
In June 2011 the ABC program
Hungry Beast produced a parody television advertisement for Qantas, highlighting the use of Jetconnect for its trans-Tasman flights.