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"The military council was not going to last forever," he said. "It is a critical battle, but this is not final."
With power now concentrated in the hands of the Muslim Brotherhood, some fear Egypt will only move from an authoritarian state to an Islamic state.
"Now the military returns to the barracks and Morsi has absolute powers," said Abdullah el-Sinawi, a prominent political commentator and longtime supporter of the military as the guardian of Egypt’s fast-fading secular traditions.
Abdel-Rahman Youssef, a liberal popular TV presenter and a supporter of Morsi, said this is a historic opportunity for political reform in Egypt.
"Egypt is now before a real test — to have a powerful president yet to stop him from being repressive," he said.
While Morsi’s Brotherhood is considered to be the country’s strongest political group, its base of support remains limited when compared to the respect enjoyed by the military. There is hardly an Egyptian family that does not include a member in active service or who had military experience. The military has a vast economic empire that accounts for about 25 percent of GDP.
But the military has been tainted in the 17 months they ran the country after Mubarak’s ouster, with the SCAF accused of mismanaging the transitional period and committing human rights violations.
For now, however, Morsi appeared the victor.
Hours after announcing the shake-up, a confident looking president appeared at an annual religious ceremony to hand monetary awards to young Muslims from Egypt and elsewhere who have learned the Quran, Islam’s holy book, by heart.
Mohammed Aboul-Ghar, a founder of the new Egyptian Social Democratic Party — a secular group critical of the military as well as Morsi’s Muslim Brotherhood — said the power struggle has now been settled in Morsi’s favor.
"The military council was forced out of power and lost its position and this was inevitable," he said. "In the power struggle, the military council was increasingly weakened because of its decisions" and its failure to secure a more straightforward path to democratic transition, he said.
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