A New Zealand wine company and three directors have been charged over a complex wine fraud involving tens of thousands of bottles, with many exported overseas, where their vintage and origin is under question.

Southern Boundary Wines Ltd, of the North Canterbury wine region of Waipara, along with its vineyard manager and winemaker Scott Charles Berry, winemaker Rebecca Junell Cope, and operations/export manager Andrew Ronald Moore, have been accused of being behind the alleged scandal.

The prosecution has been brought by the Ministry of Primary Industries (MPI) in what is understood to be the first case of its kind in New Zealand.

The alleged misconduct, dating back to 2011, 2012, and 2013 Marlborough and Waipara sauvignon blanc and pinot noir vintages, was brought to light by a whistleblower, the Herald has learned.

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The company and three directors were charged in February this year but an interim suppression order imposed by a judge prevented reporting on the case until it was lifted at Christchurch District Court this morning.

A total of 156 charges have been laid.

They include various allegations, including labelling wine as a certain vintage when in fact the grapes came from another year, false statements over where the wines came from, selling blended wines as coming from one vineyard, and trying to destroy or hide winemaking records.

Wines in question have allegedly been exported to the UK, Japan, Fiji, Thailand, and Australia.

It's understood that there is no health risk involved with any of the wine, which was made for drinking and not cellaring. None of the wine concerned is currently available for sale in New Zealand.

An interim suppression order made by Judge Stephen O'Driscoll today covers the names and brands of wines, along with the source vineyards and complainants, and the identity of the whistleblower.

The firm, 36-year-old Berry, Moore, 43, and Cope, 42, were remanded without pleas to November 30.

New Zealand Winegrowers has been advised of the MPI prosecution. The allegations, it said, are believed to be a tiny fraction of the national harvests of 2012 and 2013.

"We have been informed about the matter and the allegations and we know that MPI has been investigating carefully for some time," said Jeffrey Clarke, New Zealand Winegrowers acting CEO.

"New Zealand wineries and grape growers are committed to the highest standards of product integrity and quality, and there are very good systems in place in New Zealand to ensure this. The investigation proves the systems in place work and it is appropriate that this matter is before the courts."

New Zealand Winegrowers is concerned about the allegations and given the importance of label integrity, support the process.

"The New Zealand wine industry is highly regarded around the world and we cannot let the alleged actions of one winery damage a reputation that we have all worked so hard to build", said Clarke.