John Thomas, the head of Virgin Australia's domestic and international business, is leaving the airline less than a year after he started in the top job in what is a setback for chief executive John Borghetti's succession planning process.

Mr Thomas, a former global aviation consultant, was hired in September last year as part of a major restructure of the airline. At the time he was seen as a potential successor to Mr Borghetti, who has been running the airline since 2010.