Failure to resolve the situation 'could lead to grave repercussions if the political forces do not act' to tackle it, General al Sisi said on the official army Facebook page, as he promised to protect the country's vital infrastructure, particularly the Suez Canal.
'The continuing conflict between political forces and their differences concerning the management of the country could lead to a collapse of the state and threaten future generations,' he said in extracts of a speech to students at a military academy.
The general also warned that the political, economic, social and security problems facing Egypt constituted 'a threat to the country's security and stability'.
'The attempts to undermine the stability of state institutions is a dangerous thing that harms national security and the future of the country,' he said, adding: 'The army will remain strong ... as a pillar of the state's foundations.'
Fifty-two people have died in five days of violence that started on Thursday night, as the country marked the second anniversary of the start of the uprising that toppled former President Hosni Mubarak.
A curfew has been imposed in three provinces - Port Said, Ismailiya and Suez
The bloodiest clashes and most of the deaths have occurred in Port Said, Rioting broke out on Saturday after 21 supporters of a local football club were sentenced to death for their roles in a deadly football riot last year.
Egypt has already deployed troops to Port Said and Suez provinces, which lie at each end of the vital Suez Canal.
'The deployment of the army in Port Said and Suez aims to protect strategic infrastructure, especially the Suez Canal, which we will not allow to be harmed,' General al Sisi said, adding that the army was to assist interior ministry forces.
But, he said, the army's task was difficult. One the one hand it 'did not want to confront Egyptian citizens who have a right to protest' but, on the other, it 'has to protect vital institutions.'
Analysts say it is unlikely that the army wants to take back the power it held, in effect, for six decades since the end of the colonial period and in the interim period after the overthrow of former general Hosni Mubarak two years ago.
But, they say, it sends a powerful message that Egypt's biggest institution, with a huge economic as well as security role and a recipient of enormous US subsidies, is worried about the fate of the nation after five days of turmoil in major cities.