New Y and Xue would defend the charges, QEX said.
The charges allege that New Y and Xue in August 2019 attempted to export milk powder and honey without raising export declarations in MPI's e-certificate system in breach of the Animal Products Act 1999.
Both New Y and Xue also face three charges for attempting to export infant formula: (1) in breach of export duties; (2) in breach of risk management programmes; and (3) with intent to deceive for the purposes of a material benefit.
New Y's charges include one charge that carries a maximum fine of $500,000, with Xue's charges including a charge carrying a maximum fine of $100,000 and imprisonment not exceeding five years.
"QEX notes that the net gain from the attempted export was $2,900," it said.
"This will likely have an impact on whether the materiality threshold of the benefit in respect of some of the charges is able to be established by MPI," the company said.
MPI is scheduled to update the company and Xue's defence counsel on the future of the prosecution by the end of March.
"New Y currently holds the highest level of risk management programme standards with MPI and passed its most recent MPI audit, which was completed in November 2020," QEX said. The matter does not prevent New Y from continuing to trade, it added.
Last week, the NZX's regulatory arm - NZ RegCo - said it had suspended the quotation of QEX ordinary shares following the announcement that all QEX's independent directors had resigned with immediate effect.
Former Federated Farmers chief executive Conor English had resigned from the board, along with Danny Chan and Martin MacDonald, citing differences with Xue, who is the company's majority shareholder and the sole remaining director.
MacDonald had been appointed independent director just days before his resignation on February 18.
On the same day, New Y Trading received notice from its first ranking security holder, Westpac, that it had breached its interest cover obligation to maintain an interest cover ratio of no less than 2.50 times.
On February 10 QEX advised that the company has appointed RSM Hayes Audit as its statutory auditor following the resignation of Deloitte as its external auditor.
In its latest result - for the six months to September last year - QEX turned in a $5.86m loss.
In November, the company said it was investigating missing inventory, presumed stolen, from a Shanghai bonded warehouse, worth $4.3m.
QEX listed on the exchange's then small-cap NXT in 2018.
Before its suspension, the stock traded at 28.5c, having fallen by 60 per cent over the previous 12 months.