A Hillsong whistleblower has alleged she was unlawfully disciplined for sharing information with Australia's charities regulator during an investigation into the global church's account.  

In August, news outlet ABC revealed the Australian Charities and Not for Profits Commission (ACNC) had launched an investigation into the church's financial practices following claims of financial misconduct made by former employee Natalie Moses. 

This week, lawyers defending Moses told the court that Hillsong Church's chief financial officer directed her about what "should be reported or should not be reported" to the ACNC.

"There appears to be a concern (from Hillsong) as to whether my client was providing information to the ACNC," Philip Boncardo said.

"As a result of those concerns, my client was effectively stood down and required to provide information in her possession to (her employer)."

Boncardo argued Moses had exercised her right to make a complaint to the regulator and her suspension was considered to be adverse action, a legal term referring to when an employer's position towards an employee changes as the result of new information discovered. 

Hillsong Church, it's subsidiary Hillsong CityCare and Hillsong CFO Peter Ridley are due to file their defences by 21st October.

In a statement to ABC after their investigation, the church's lawyers said: "We are further instructed that Hillsong is continuing to work with the enquiries made by the Australian Charities and Not-for-Profit Commission."

"As the matter is now before the Federal Court of Australia, it is inappropriate to make any further comment."

The matter is due to return to court on 6th February.