A whistleblower suing Hillsong has claimed that the religious organisation avoided difficulties with the Australian charities regulator by moving money through overseas entities, an ABC investigation has revealed.

According to the news outlet, the Australian Charities and Not-for-Profits Commission (ACNC) launched an investigation into the megachurch in March.

As Hillsong is a registered charity, the ACNC were looking into its compliance with the rules to which such organisations must abide.

The commission’s investigation came to light after a former employee of Hillsong, Natalie Moses, launched a Fair Work case against the church.

Within her complaint, she alleges financial malpractice, including using tax-free money for “large cash gifts” to former Hillsong global leader and founder Brian Houston, and members of his family.

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."