The Australian pastor and founder of a global Pentecostal megachurch has pleaded not guilty to concealing his father's alleged child sexual abuse.

Hillsong Church pastor Brian Houston, a prominent Australian religious figure with ties to the country's conservative prime minister, is accused of failing to report the abuse of a young boy after learning of the claims in 1999.

His father, Frank, who died in 2004, has been accused of sexually abusing a seven-year-old boy while a preacher at the Assemblies of God church in the 1970s.

At a brief court hearing in Sydney, lawyers for Mr Houston entered a plea of not guilty on his behalf.

He has previously rejected allegations of a cover-up and vowed to clear his name, saying he confronted his father about the claims but did not go to the police, in line with the alleged victim's wishes.

Australian Prime Minister Scott Morrison, who has attended Hillsong Church events, said in a statement when the charges were announced that it would be "inappropriate to comment" on the case.

Hillsong Church operates in 30 countries and claims an average weekly attendance of 150,000 people.