The IAAF, the governing body for athletics, said that Clothier would be in charge of the unit's "core activities" which included "testing; intelligence and investigations; compliance; case management and education."
Clothier previously established a similar unit to monitor doping, match-fixing and other integrity issues in Australian rules football, which he then led for eight years.
"I am excited by the opportunity I have been given to lead the athletics integrity unit in rebuilding athlete and fan confidence in how we manage threats to the sport," said Clothier in an IAAF statement.
The AIU is a plank in the sweeping reforms introduced by IAAF president Sebastian Coe after a series of scandals, including a corruption probe by French authorities into high-ranking officials such as his predecessor Lamine Diack.
A doping scandal involving Russian athletes, which saw the country's track and field team banned from last year's Rio Olympics, has also cast a long and enduring shadow over the sport.
New Zealander David Howman was named as the AIU's chairperson in April.
"(Clothier's) track record of establishing and driving forward the Australian Football League Integrity Unit from scratch eight years ago speaks for itself," he said.
"He is the ideal person to lead the AIU’s athlete-centred programs during this crucial period for our sport."
(Editing by Amlan Chakraborty)
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