New South Wales land owners have been warned to be cautious when accepting landfill, after the disappearance of 600 truckloads of waste material containing asbestos from a Sydney development site.

It is alleged contractors removed the restricted material from August 2016 as part of the Green Square Town Centre development.

NSW Police, along with the NSW Environmental Protection Authority (EPA), began investigating after noticing "anomalies" in the waste removal record.

A 48-year-old man was arrested at the Sydney International Airport last Friday while attempting to leave the country, and he was charged with more than a dozen fraud-related offences totalling $4 million.

But police on Thursday admitted the whereabouts of the 17,000 tonnes of waste remains unknown.

The man will appear in Central Local Court this Friday to face 13 counts of dishonestly obtaining financial advantage by deception, knowingly dealing with the proceeds of crime and knowingly directing the activities of a criminal group.

The NSW Environmental Protection Authority has helped police investigate the disappearance of the waste. ( Supplied: NSW Police )

Assistant Commissioner Mark Waldon said police had frozen several bank accounts.

He also issued a warning to land owners in the region.

"If you are approached to receive waste material on your land, take care," he said.

Police suspect the asbestos-filled material has been illegally disposed of. ( Supplied: NSW Police )

"Those involved in this illegal practice will misrepresent the waste and you may be left with land that has no value."

The EPA's Mark Gifford said the illegal dumping of asbestos could attract penalties of up to $5 million, in addition to jail sentences.

The current matter was one of the largest the EPA had investigated, he added.

"Waste crime is a significant issue and one that we have taken seriously enough to develop and implement a waste crime taskforce in the EPA," he said.

Police on Thursday searched a home at Kemps Creek in relation to the case, seizing documents and computers.

Officers have also recovered other evidence from properties in Smithfield, Guildford West and Merrylands West.