Director-general Somchai Sujjapongse said the quest began two months ago after he took office and some 100 supercars whose owners had dodged import duties were found.
In normal practice, supercar importers park the cars in bonded warehouses.
The vehicles are taken out to be put on display and taxed once they are sold or stored in a bonded warehouse for more than a year.
Mr Somchai said he thought the lost supercars might have been sold without a customs tax payment.
After the supercars disappeared from the bonded warehouses, he set up a committee to examine the case.
Two customs officials have since been reassigned.
Similarly, import duty avoidance has been detected in the superbike sector.
The department has already collected tax on 80 superbikes.
The problem of smuggled luxury cars has entered the spotlight several times, with the latest tax-evasion probe launched last year.
"It's worrisome, because they may disappear for a long while," Mr Somchai said.
"Since it happened during my term, I've instructed officials to tighten checks on imported products from China and supercars and to set up a committee to investigate cases."
The director-general has floated the idea of requiring each supercar taken out of a bonded warehouse to be equipped with a radio-frequency identification tag and GPS module to track the car's location.