In a live speech broadcast nationwide, Prime Minister Hazem el-Beblawi said: "The government made every effort to get Egypt out of the narrow tunnel in terms of security, economic pressures and political confusion."
Mr Beblawi, who was tasked by interim president Adly Mansour with running the government's affairs until the election, did not give a clear reason for the decision.
To run for president, Mr Sisi would first have to leave his post as defence minister.
One official said: "This government resignation was done as a step that was needed ahead of Sisi's announcement that he will run for president."
The official said the cabinet resigned en masse as Mr Sisi did not want to appear to be acting alone.
The top military commander has unveiled a political roadmap meant to lead to elections following the ousting of Islamist President Mohamed Mursi last July.