The defendants entered not guilty pleas through their counsel and were granted bail until the next court hearing in three weeks' time, when the interim name suppression orders will be argued.
Judge Gibson initially said he wasn't perturbed by the formality of having the six accused stand in the large, glass-windowed dock.
"They should be in the dock, but this shouldn't take too long, so I won't insist," he told counsel.
However, Judge Gibson later did insist on the six moving from the public gallery to the dock to allow photojournalists the opportunity to film them.
Prominent Auckland barrister Paul Wicks QC is prosecuting the case for the SFO.
Court documents earlier released to media by the Auckland District Court show the six people face 12 total charges.
The SFO filed the charges on May 12 after an investigation into donations made to the Labour Party in 2017.
Each of the accused are charged with two counts of obtaining by deception over a donation of at least $34,840 for the Labour Party on about March 28, 2017. The SFO alleges the identity of the donor was not disclosed in the party's annual return of party donations.
The group are accused of adopting a "fraudulent device, trick or stratagem" where the donation was paid via an intermediary account before being paid to, and retained by, the Labour Party.
Court papers also allege the group provided five names to "create the illusion" of five donations of sums of less than $15,000 to conceal the amount and identity of the actual donor.
The accused six are also further charged with unlawfully obtaining a benefit for the true donor by allowing them "freedom from any public scrutiny".
After the charges were filed, Labour Party general secretary Rob Salmond said in a statement the party has "complied with the law."
Prime Minister and Labour leader Jacinda Ardern also commented to reporters by indicating there was something wrong with the legislation because so many political parties are facing legal action.
"This isn't a good environment for anyone, for no political party, but nor for New Zealanders, they want to have confidence in the system, so let's look at the law," she said.
"That sends a message to us, in the political system, that we should be looking at the way our regime works."
There are separate SFO prosecutions involving the National Party and the NZ First Foundation, while the Māori Party is under investigation.
Auckland Mayor Phil Goff's campaign expenses are also the subject of an SFO investigation.