Mursi, who was ousted in July 2013, faces trial alongside 10 others, including two of his aides over accusations of leaking classified national intelligence to the Qatari intelligence.
After deciding on the secrecy of today’s session, in which defendants’ possessions were shown, the court asked that everyone except for the defendants and their defense team vacates the chamber.
The court said it ordered that the session be confidential, "in accordance with its rights," as stipulated in the law.
This trial started last month, with Mursi saying in the first hearing that he was brought to court "forcibly".
Egypt’s top prosecutor referred Mursi, the head of his presidential office Ahmed Abdel Aati and his personal secretary Amin al-Serafy and the eight others to court on September 6, 2014.
Mursi has refused to answer questions on this case during investigation.
Prosecutor General Hisham Barakat accused Mursi and his two aides of seizing classified national security intelligence and delivering them to the Qatari intelligence and the Qatari news network al-Jazeera.
He said they leaked the intelligence with the help of eight "spies" and in exchange for a million dollars, adding that they were carrying out the instructions of the "terrorist" Muslim Brotherhood international organisation.
Egyptian-Qatari ties have been strained since Mursi’s military ouster, with the authorities replacing Mursi’s regime viewing Qatar as a Brotherhood sympathiser, using the Qatari Al Jazeera network for this aim.
Egypt’s former president was ousted by the military after mass protests against his rule.
Mursi, who now stands trial in a total of five cases, faces an array of charges and was already facing espionage charges before this trial began.
He is also accused of inciting to kill protesters outside the presidential palace during his tenure, insulting the judiciary and escaping prison during the January 2011 uprising.
Since Mursi’s removal, the Brotherhood has faced a severe crackdown and the group’s leaders are featured in these trials alongside Mursi.