Quiboloy's lawyer Israelito Torreon said he pleaded "not guilty" at the brief Manila court hearing, from which journalists were barred .
Four other detained sect members also pleaded not guilty.
Quiboloy and the others also pleaded not guilty via video conference on separate child abuse and sex abuse charges in a separate Manila court later Friday, his lawyer said.
Following his arrest in Davao, police said more victims, including girls as young as 12, have come forward to allege sex crimes committed against them by the pastor.
The young victims were told they were having sex with the "Spirit of God", and were threatened not to tell anyone on pain of being hunted down by "angels of death", Philippine police spokeswoman Colonel Jean Fajardo told reporters on Thursday.
Quiboloy's Kingdom of Christ Church said on its website that members have "freedom of choice" and thus "anything that happens to you... is your own voluntary will or choice".
The powerful sect claims millions of followers in the mainly Catholic Asian nation and owns a television network.
Women and children advocate Senator Risa Hontiveros said in a statement Friday that Quiboloy must be held accountable.
"He and his co-accused have caused unspeakable pain to women, children, and the most vulnerable," she said.
President Ferdinand Marcos said Monday the government was not yet looking to extradite the pastor to the United States, because "we are focusing on the cases filed in the Philippines".