He told the court that he refused to be tried as he remains Egypts legitimate president.
Mursi also chanted: Down with military rule, according to local press reports.
The judge brought the trial to a halt shortly after his comments, and delayed the proceeding until early 2014.
Mursi was being tried alongside 14 other senior members of the Muslim Brotherhood, charged with inciting the killing of demonstrators last December during protest marches outside the presidential palace.
Mursi was ousted from power on 3 July by the military following mass protests against the Muslim Brotherhood-backed leader. Mursi had only been in power less than a year, but stood accused on mismanaging Egypts economy and giving the brotherhood too much power within parliament.
The trial follows US secretary of states John Kerry visit to Egypt on 3 November.
During his stay, Kerry re-emphasised the need for Egypt to restore democracy to the country.
One thing I cant stress strongly enough, and that is the link between Egypts progress in its democratic transition and its overall economic success, he said.
US-Egypt relations have been strained since Mursis ousting and the subsequent violent clampdown on pro-Brotherhood supporters. The deaths of at least 900 people during clashes in mid-August led to the US suspending military aid to the country.
During a press conference, Kerry did make encouraging comments about Egypts process to moving toward democracy.
The roadmap is being carried out to the best of our perception, he said.