Cho Yang-Ho is under investigation for allegedly using three billion won (US$2.65 million) allotted for the construction of a new hotel to pay for the remodelling of his house in 2013.
An arrest warrant has been requested on charges of breach of trust, a police official said.
Hanjin Group is one of South Korea's largest companies and the parent of Korean Air, the country's flag carrier.
But it has faced repeated troubles in recent years.
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Cho last year stepped down from heading the organising committee for the 2018 Winter Olympics in South Korea to address the "critical financial issues" at the unit.
His daughter Cho Hyun-Ah was jailed in 2014 following a meltdown on board a Seoul-bound Korean Air flight that had just left the gate in New York.
As the plane was taxiing to the runway, Cho, sitting in first class, became enraged when a flight attendant served her some nuts in a bag, rather than on a plate.
She was eventually convicted of hampering the aircraft's operations and violence against cabin crew members.
In connection with the current investigation authorities raided the Korean Air headquarters last month and questioned Cho Yang-ho for 16 hours.
Korean Air spokesmen could not be reached for comment.