The man is in custody and appeared via audio-visual link.
He was arrested in June and appeared at Christchurch District Court.
Police allege he repeatedly sexually violated and performed indecent acts on a child aged under 12.
The man also faced numerous charges of making objectionable videos, of various length, including one nearly six minutes long which allegedly shows him raping the child.
Initially he faced 50 charges but by the time he appeared in court today that total had reached 80.
The charges included allegations he was found in possession of thousands of child sex abuse images and videos as well as claims he made child exploitation images.
Judge Couch confirmed this afternoon that 40 of those charges would be withdrawn.
He did not specify which of the 80 charges were dropped immediately in court today but indicated he would do so.
Suppression orders currently cover the man's identity, his alleged victim, and his employers.
A hearing has been scheduled for November for a judge to properly hear full arguments around suppression.
The Crown indicated it opposed name suppression and did not believe the alleged sex offender had reached the threshold needed to prove extreme personal hardship.
The company he is employed by is seeking permanent name suppression separately from the alleged offender as a connected party.
Both applications for suppression will be heard on November 15.
The man indicated previously that he wished to represent himself, believing that he would not be eligible for Legal Aid.
But a judge urged him to make inquiries into whether he was indeed eligible to receive Legal Aid and get a lawyer to represent him on he said what were "undoubtedly … very serious allegations".
He is now being represented by defence counsel Andrew McCormick, who appeared for him in court this afternoon.
