"This is the first time I see Ethiopian Muslims united against their common enemy," Temam Mohammed, one of the protestors, said.
"The ‘Majlis’ leaders thought they can impose their evil policy on us by using force," he said, referring to the Supreme Council of Islamic Affairs.
Thousands of Muslims protested across the capital Addis Ababa following the Friday prayers to protest the government oppression of their community.
Chanting "We want our rights" and Allahu Akbar (God is Greatest), the protestors condemn government restrictions on their community.
Protestors say the government is spearheading a campaign in collaboration with the Majlis to indoctrinate Muslims with the ideology of a sect called "Ahbash".
The government of Ethiopian Premier Meles Zenawi has put the Ahbas in charge of the religious affairs of Ethiopia's Muslims.
Muslims say the government move was in violation of the constitution, which prevents the government interference in religious affairs.
Muslims also accuse the Ahbash of launching an "indoctrination program" in predominantly Muslim areas, forcing people to attend "religious training" camps or risk police interrogation and possible arrest.
"They thought they can draw a line between "Sufi” and "Salafi” and fulfill the interest of Ahbash which is a deviant business motivated sect seeking to expand its empire by dividing the people," Mohammed said.
"But we were fast enough to know their hidden agenda and strengthened the brotherly bond among the Muslim society. That is why you see this large mass coming here to demand its right."
Founded by Ethiopian-Lebanese scholar Sheikh Abdullah al-Harari, Ahbash is seen by the West as a "friendly alternative" to Wahabi ideology, which the West sees as extreme and militant.
Muslims say Ahbash imams are being brought over from Lebanon to fill the Majlis and teach Ethiopians that "Wahabis” are non-Muslims.