Tax Office second commissioner Andrew Mills will leave the job at the end of the year, a year before his term ends.
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A spokesman confirmed on Friday that Mr Mills "has decided to retire from the Office of Second Commissioner of Taxation effective 31 December 2019".
Mr Mills is second commissioner responsible for the Tax Office's law design and practice group, including law interpretation and prevention and resolution of disputes.
He was appointed as second commissioner in December 2013, his term to run until December 2020.
The office, headed by Commissioner Chris Jordan, has three second commissioners.
The others are Ramez Katf, in charge of technology, and Jeremy Hirschhorn, who has been acting as commissioner responsible for client engagement since December 2018, according to the website.