David Jones QC, who is representing the 59-year-old defendant, said his client has been issued with an order by Malaysian authorities not to leave the country.
An arrest warrant for the man, who watched the hearing through a screen, had earlier been issued by the Auckland District Court in February.
Jones told the court that today's hearing was effectively the first for his client and asked Judge Ryan to proceed with the administrative aspects of the case - in absence of the man being in New Zealand.
The man faces six charges for money laundering, obtaining by deception and causing loss by deception. Jones entered not guilty pleas on his behalf today.
The second defendant, a 54-year-old man, failed to appear via video link today and is understood to currently be on a Pacific island. He faces three charges, which Judge Ryan said were yet to have pleas recorded.
The judge added that she was "somewhat concerned about his lack of appearance today".
She decided to grant interim suppression for both men until a further hearing in October.
The OFC has said in an earlier statement it could not comment while the case is before the courts.
The SFO has been probing the OFC for years, following allegations of kickbacks and corruption during the past decade. Former officials have been fined and banned from further involvement in the sport by Fifa.
International football has been marred in recent years with allegations of corruption over its awarding of World Cup hosting rights and the resignation of former Fifa president Sepp Blatter, who faces prosecutions for bribery and fraud.