Governor Basuki "Ahok" Tjahaja Purnama, an ally of President Joko Widodo, faces up to five years in prison if found guilty.
He wiped away tears as he gave his initial statement to the court.
"I understand the charges but I don't understand why I'm being accused of blasphemy," he said after prosecutors read out the indictment.
The blasphemy controversy erupted in September when a video circulated online in which Ahok said people were being deceived if they believed his detractors who asserted that the Koran prohibits Muslims having a non-Muslim leader.
He is seeking a second term as governor in elections due February.
Anti- and pro-Ahok groups have gathered outside the court.
A November 4 protest in Jakarta against Ahok turned violent, with one death and dozens injured.
