The court heard Mr Willis, working for the Public Defence Service, had been assigned to Fomai but not the church because it wasn't considered a legal person.
"I don't think you can charge a church... to do something false requires a human to do it," Judge Tuohy said.
Appearing on behalf on the informant, the Ministry of Business, Innovation and Employment, crown prosecutor Steve Manning said the charges had been laid against the church because it was listed on the Charities Register and Fomai was its certification officer.
The judge said surely someone had twigged to the issue of whether the church was a legal person or not, adding he was "not really happy" about the fact the church had so far received no representation.
"It seems to me that the [informant] needs to be in a position to tell the court that the church is a registered charity, somehow a legal person."
The church and its pastor are alleged to have brought Mr Siatulau, a Samoan police officer, to New Zealand on the pretence that he would work as a youth pastor in 2015.
In September last year the Immigration and Protection Tribunal heard the father of five arrived to find the church barely existed beyond the pastor and two couples, and that he could not be paid as a youth pastor and would instead be working in an orchard.
He claimed he had been exploited, and that he and his family had been "victims of the pastor".
Everlasting Gospel Church, and Fomai, were remanded for a final time to appear again on October 10.
Judge Tuohy noted there had been some confusion between the church and its pastor. That matter is set to be resolved in October.