Brian Houston, who was born and raised in New Zealand, was charged in October last year with one count of concealing the serious indictable offence of another person.
The founder of Hillsong made the announcement today, after last year stepping aside as director of all Hillsong boards.
He said he intends to vigorously defend the charge.
His father, Frank Houston, was allowed to retire from the church before the allegations of the abuse of a young man became public, and died in 2004.
In a statement on the church's website, Brian Houston said the charges were "unexpected" and the allegation he had failed to disclose information about his father had come as a "shock".
Houston also said his latest decision came after discussions with the board last month.
"In December, during our board meeting, Hillsong's external legal counsel gave the board advice regarding the current charge I am facing," Houston said.
"That it would be 'best practice' for me to step aside completely from church leadership during the court proceedings.
"The court processes are likely to be drawn out and take up most of 2022 [especially considering the backlog in the courts, exacerbated by the Covid-19 pandemic]."
The 67-year-old, who is due to appear before a Sydney court in October, said his emotional wellbeing was also a factor.
"We have talked about the effects of the situation with my father, which go back many years up to the current legal case, and the impact this has had on me emotionally."
Houston said he would use the time to work with his legal team to set the record straight.
Police have previously alleged their investigation into Brian Houston began in 2019.
The Royal Commission into Institutional Responses to Child Sexual Abuse heard Frank Houston admitted to the abuse, which took place in Australia and New Zealand.