Mr Shafiq, a former air force commander who came second in last year's presidential election, said he would not run if Mr Sisi stood in the election, which is expected next year.
His comment suggests why, just months before the election, there are no declared candidates as politicians wait to see if Mr Sisi is going to run before announcing their own intentions.
Former Arab League chief Amr Moussa, who also ran in last year's poll, said Mr Sisi would win by a landslide.
Egyptians had become "angry and afraid of anarchy and terrorism" and wanted a decisive leader, he said.
Mr Sisi has said he does not seek authority, though speculation that he will run has mounted since he toppled the Muslim Brotherhood's Mr Mursi from the presidency on July 3.
Mr Shafiq said he would not contest an election if Mr Sisi did run.