CAIRO (CNN) -- Egypt's interim military government added the Muslim Brotherhood's spiritual leader Tuesday to its list of the movement's top figures under arrest.

In a dawn raid, followed by the storming of a school facility and activity around the country, the government arrested nearly 100 members of the Muslim Brotherhood, which is locked in a deadly battle with the military for control of Egypt.

Mohamed Badie, the group's spiritual leader, was taken into custody at a residential apartment in Cairo's Nasr City neighborhood at dawn, the Ministry of Interior said.

The brotherhood slammed the arrest as part of "a bloody military coup."

Arresting Badie "is not the end of the group, which will remain in the hearts of millions of Egyptians," Ahmed Arif, spokesman for the Muslim Brotherhood, said in a statement.

Mahmoud Ezzat, Badie's deputy, was named supreme guide on a temporary basis.

The military has been arresting numerous key figures in the Muslim Brotherhood, including Mohamed Mahdi Akef, the former supreme guide; his deputy, Khairat al-Shater; Saad al-Katatni, chairman of the brotherhood's Freedom and Justice Party; his deputy, Rashad al-Bayoumi; and Sheikh Hazem Salah Abo Ismael.

Armed fighters holed up in school facility, military says

Badie is accused of inciting violence, according to state-run Nile TV.

He was with Syed Abdul Rahim Abdel Naby, a teacher from the Islamic Dawa school in Beni Suef, when he was arrested at dawn, the Ministry of Interior said in its statement.

Security forces then searched the school and arrested 38 members of the Muslim Brotherhood "who were hiding" in the facility and had numerous weapons, including a rifle, pistols, and Molotov cocktails, the statement said. Some of the equipment belonged to the administration of the civil protection unit in Beni Suef, which had been stormed, robbed and set on fire, the statement said.

Both sides in the conflict have insisted they reject violence, but fighting has raged.

The Muslim Brotherhood changed its profile image on Facebook Tuesday to an image of Badie, with a quote saying, "Our peaceful movement is mightier than their tanks."

Nationwide arrests

Security forces also arrested 56 administrative leaders of the Muslim Brotherhood in various provinces, the Ministry of Interior said.

The arrests came a day after 25 soldiers were killed in a Sinai ambush and onetime ruler Hosni Mubarak won acquittal on a corruption charge.

The soldiers were killed when suspected militants armed with rocket-propelled grenades struck two buses carrying security forces Monday in the city of Rafah, on the border between Egypt and Gaza, Nile TV reported.

Interim President Adly Mansour declared three days of national mourning following the attack, Nile TV said.

The Sinai Peninsula is a lawless area that was the site of frequent attacks even before Egypt's latest round of turmoil. In May, for example, seven Egyptian solders were kidnapped and held for six days there, a spokesman for Egypt's armed forces said.

But the attack adds to the persistent tension across the country since the military ousted democratically elected President Mohamed Morsy in a coup.

Over the past week, about 900 people -- security personnel as well as citizens -- have been killed.

Deaths occurred when the military used force to clear two pro-Morsy sit-in sites in Cairo on Wednesday and violence raged after pro-Morsy supporters staged demonstrations Friday.

CNN's Saad Abedin reported from Cairo; CNN's Mohammed Tawfeeq, Ali Younes, Schams Elwazer, Ian Lee, Reza Sayah, Hamdi Alkhshali, Slma Shelbayah, and Holly Yan contributed to this report.