Kuwait newspaper Al-Seyassah had published what it said was an interview with Sisi, in which the 59-year-old general was quoted as saying that he "would fulfill people's demands to run in the presidential election" due to be held before mid-April.
But army spokesman Colonel Ahmed Ali said: "What was published in Al-Seyassah is merely journalistic speculation and not a direct statement from Field Marshal El-Sisi." He described the report as "inaccurate".
Ali's statement called on local and international media to be careful while disseminating news about the military and its leaders.
Sisi, recently promoted to Field Marshal, was last week given the green light by the powerful military council to contest the first presidential elections after the army toppled Islamist president Mohammed Morsi in July last year amid mass protests against his rule.
Widely popular for overthrowing the Islamist regime linked to the now outlawed Muslim Brotherhood, Sisi, also the Defence Minister, is expected to win polls easily as he has no serious rivals.
Sisi was expected to step down as the army chief before contesting the election scheduled to be held between February 17 and April 18 under a new constitution passed last month.
Under his leadership, the Egyptian army cracked down on the Brotherhood and Islamist militants, killing scores of them.
Sisi said that if he wins, he would call for a pan-Arab alliance to fight against growing "terrorism" in the region.
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