His twin brother is now expected to face charges of being an accessory after the fact.
He will appear in Sydney Central Court on Thursday.
Stephanie Scott, an English and drama teacher, was last seen by a colleague at Leeton High School on Easter Sunday.
Police allege that Vincent Stanford killed Ms Scott on that day, dumping her car and body afterwards.
Investigations into her death focused on Stanford after he was found to have given allegedly misleading information to authorities about being at the school on Easter Sunday, the Daily Telegraph reported at the time.
Police searched his home, which he shared with his mother and older brother, where they allegedly found a set of keys given to Ms Scott on Easter Sunday.
The keys were reportedly given to Ms Scott so she could enter a classroom to finish off lesson plans for a substitute teacher.
Ms Scott was planning to go to Tahiti on her honeymoon after marrying her fiancé, so was preparing for her absence.