A Dunedin businessman who allegedly altered invoices to undervalue imported heavy machinery and evaded paying at least $1.4 million in GST at the border has been arrested following a Customs raid.

According to court documents, Paul Lambert Clarke, 43, of Mosgiel appeared in the Dunedin District Court today facing three charges, including defrauding Customs revenue, offences in relation to declarations and documents that are known to be faulty, and obtaining by deception.

About $6 million of property has also been seized by the Southern police asset recovery unit.

Customs began investigating his business earlier this year after discovering that he had used an altered invoice to significantly undervalue an imported consignment of heavy machinery, Customs said in a statement.

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An initial audit of 25 imported consignments by Clarke's company showed that most of the consignments had been undervalued.

Customs records show the business had imported more than 200 consignments since 2013, and the undervaluations were believed to have spanned the six-year period.

An initial analysis of the imported consignment documents show that at least 90 of them had been undervalued, by a total of $9.6 million, resulting in $1.4 million in GST payments being evaded.

Customs investigators, assisted by police, carried out search warrants in Dunedin and Cromwell today leading to the man's arrest.

Customs investigations manager Bruce Berry said the accused had deliberately tried to circumvent the border systems in place to collect Government revenue.

"Defrauding Customs of revenue is fraud and a serious crime, with a penalty of up to five years in jail.

"Heavy machinery doesn't attract additional tariff duties, but GST must still be paid. All businesses should be aware of this, and fraudsters will be prosecuted.''

Police asset recovery manager Detective Senior Sergeant Brent Murray said police asset recovery units will work closely with all law enforcement agencies to ensure people do not financially benefit from their criminal activity.

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"Working closely with NZ Customs ensures that whatever the crime the criminal proceeds recovery act is about ensuring that crime does not pay.''