Hillsong's interim lead pastor, Phil Dooley, has confirmed the church has been sued by a staff member.
"This case involves employment issues, however, it includes various allegations that pertain to church finances," Pastor Phil wrote in a message to the church.
"While I'd like to provide you with more specific details I, unfortunately, cannot, because while the claims can be publicised, it is inappropriate to respond or comment publicly because the matter is before the court."
It follows earlier reports by Australian news outlet ABC News that a staff member had brought a lawsuit against Hillsong Church for avoiding difficulties with the Australian charities regulator by moving money through overseas entities.
The staff member, who has been named by ABC News as Natalia Moses, claims the religious organisation used tax-free money for "large cash gifts" to former global leader and founder Brian Houston and his family.
Houston resigned from his role in March after allegations of misconduct toward two women. He had been previously gone on leave to concentrate on fighting his legal case in which he stands accused of covering up the historic child abuse of his father.
In his response, Pastor Phil said he will chair a meeting on Tuesday to share the progress "Hillsong Church is making to bring significant change to our organisational structure".
He also reminded the congregation that the content of the lawsuit are currently "allegations" that are "untested and unproven".
"But equally, I want you to know that if throughout this process we find that we need to make changes, we will. We are confident that truth will prevail, and we appreciate your prayers."
He continued: "This is a new day for Hillsong, and we are today a different church to what we were even a year ago. When issues like this arise, our first response must be to look to the Holy Spirit and be led by Him.
"Please keep in mind that anything you may hear, or that may be reported, are allegations that are untested and unproven. But equally, I want you to know that if throughout this process we find that we need to make changes, we will. We are confident that truth will prevail, and we appreciate your prayers."