Egyptian military spokesman Ahmed Ali said an article published in the daily newspaper al-Siyasa was conjecture, not a statement from al-Sisi, Ahram Online reported.
"What was published in al-Siyasa is merely journalistic speculation and not a direct statement from Field Marshal al-Sisi," Ali posted on his Facebook page.
In the article, al-Sisi was quoted as saying he "would fulfill the people's demands to run for president."
"Egyptians have big dreams and in order to fulfill those dreams we need everyone to help and cooperate. Some rulers disturbed the country by using their position to serve their own interests," al-Sisi was quoted as saying in an apparent reference ex-President Mohamed Morsi, who was ousted in June.
"We don't have a magic wand but we will not tamper with the people's dreams and aspirations," he was quoted in the article as saying. "Let's hold our hands together and work for the country."
The military council recently gave al-Sisi, also Egypt's defense minister, the OK to run in Egypt's first presidential elections since Morsi was toppled in July amid anti-government protests.
Ali's statement said the decision would be "personally taken [by al-Sisi] in front of the great Egyptian people, clearly and directly, without doubt or speculation."
Al-Sisi, recently promoted to field marshal, is expected to leave his post before entering the presidential race, Ahram Online said.
Presidential voting is expected to be conducted sometime between Feb. 17 and April 18. Interim President Adly Mansour decided to conduct the presidential election ahead of the parliamentary balloting, changing the transitional road map.