Protesters at the Khartoum sit-in, meanwhile, said the council's reforms did not go far enough and called on the ruling body to hand over power immediately.
Earlier on Sunday, the military council met with some political parties in Khartoum and urged them to agree on an "independent figure" to lead Sudan as prime minister.
In his first televised address as de facto leader of the country on Saturday, he said that a civilian government would be established following consultations with opposition forces, promising that the transitional period would last for a maximum of two years.
"The steps taken by the army on Thursday, April 11, take the side of the people for the sake of freedom, peace and justice", the ministry said, echoing one of the protesters' slogans.
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"We congratulate our people on this historical victory and the victory of our will, but we believe that the time for leaving the squares has yet to come - until power has been transferred to a civilian council within a clear transitional arrangement between the revolutionary forces in the army and the political parties", she said.
Saudi Arabia and the UAE have already expressed support for Sudan's new military leaders.
"We demanded restructuring the current security apparatus", el-Digair said.
Saudi King Salman ordered an unspecified package of aid for Sudan that includes petroleum products, wheat and medicine.
Gen. Abdel Fattah al-Burhan vowed to "uproot" deposed president Omar al-Bashir's regime and release protesters, in a bid to placate demonstrators demanding civilian rule.
The military council later held a press conference at which its spokesman did not respond to the protesters' latest demands. The council will also form a committee to take over the assets of al-Bashir's party, he added.
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"The ministry of foreign affairs is looking forward to the global community to understand the situation and to support the transitional military council.in order to achieve the Sudanese goal of democratic transition", the ministry said in a statement.
"It is crucial that Sudan's new authorities investigate Salah Gosh's role in the killings of scores of Sudanese protesters over the past four months", Amnesty said in a statement. Protesters fear that the military, which is dominated by al-Bashir appointees, will cling to power or select one of its own to succeed him.
General Awad Ibn Ouf made his announcement on Friday through the state television, leading to the crowds shouting in jubilation.
Al-Bashir imposed a state of emergency in February, banning unauthorized public gatherings and granting sweeping powers to the police in an effort to quash the protests.
Dozens of people have been killed in protest related violence since demonstrations erupted against Bashir's rule in December.
The face of the coup, ibn Ouf was himself head of military intelligence during the brutal campaign to suppress the Darfur insurgency.
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