The court's decision came two months after it referred the case against the Brotherhood's general guide Mohamed Badie and hundreds of others to the state's highest religious authority, the Mufti, the first step towards imposing a death sentence.
Lawyers said the ruling can be overturned on appeal. It was not immediately clear how many sentences had been confirmed, with lawyers giving estimates ranging from 182 to 197.
Lawyers boycotted the opening of the trial on March 25 to protest an earlier mass death sentence by the judge. A month after that session, the judge sentenced 683 people to death, including the Muslim Brotherhood's Supreme Guide Mohammed Badie.
The case is rooted in retaliatory attacks on a police station in the southern city of Minya on Aug. 14, after police dispersed an Islamist sit-in in Cairo, killing hundreds.
An Egyptian court signaled on Thursday that it wanted death sentences for Badie and 13 other defendants charged with murder and firearms possession, when it referred the case to the country's religious authorities.
Judicial sources said a judge at a court in a Cairo suburb referred all 14 of the defendants to the Mufti, the highest Islamic legal official, who must give an opinion on death sentences before they can be confirmed.
More than a thousand suspected supporters of Morsi and his Muslim Brotherhood have already been given death sentences this year which were referred to the Mufti. Their cases have provoked outrage among rights groups and Western governments.
Thirty-seven of the sentences have been upheld, and more than six hundred others are awaiting a final decision. But so far none of the sentences has been carried out.
The court decision came less than two weeks after former army chief Abdel Fattah al-Sisi took office as president. Sisi ousted President Mohamed Morsi of the Brotherhood last July, leading to a widespread crackdown on the movement.
Badie, who faces charges in several other cases, has already been referred to the Mufti on another set of charges.
Among the defendants were senior Brotherhood members Mohamed El-Beltagi and Essam El-Erian and former members of the Morsi government.