"I hope he stays in the army. And someone else [stands] for the presidency," Sheikh Mohammed bin Rashid al-Maktoum said in an interview with the BBC, excerpts of which were provided today by the channel.
"That's what I think," he added, when asked again if he thought Sisi should stay in the military instead of becoming the head of state.
But a UAE government spokesperson tried to soften Sheikh Mohammed's remarks, stressing the "UAE's respect for will of the Egyptian people and support for their political choices."
Sisi had said on Saturday that he would stand in the presidential election slated for the autumn if the public and military backed his candidacy.
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"If I nominate myself, there must be a popular demand, and a mandate from my army," the state newspaper Al-Ahram quoted Sisi as saying on Saturday at a meeting with Egyptian officials.
Sisi is the most popular leader in Egypt after toppling Islamist president Mohamed Morsi in July, and military officers have told AFP he had support within the army to stand in the election scheduled to take place by the autumn of 2014.
Dubai is one of seven emirates that form the federation of the United Arab Emirates, which backed Egypt's military-installed government with billions of dollars.