State television showed a pale-looking Mubarak, smiling as members of parliament stood to applaud his return to the chamber of the People's Assembly before he resumed his speech.
He spoke about the crisis in the Middle East before terminating his speech five minutes later and leaving again.
Information Minister Safwat al-Sharif said the 75-year-old president was suffering from "a severe 'flu, accompanied by fever".
Earlier, Mubarak was seen coughing, pulling out a handkerchief and wiping perspiration from his brow moments before state television cut the broadcast of his speech for several minutes.
Sound transmission continued for seconds longer than the picture, with coughing and shouting heard.
When the broadcast of the assembly resumed, Mubarak was absent from the podium and a television announcer reported the president had suffered a "minor health problem".
The assembly speaker, Fathi Srur, told the chamber "the president is fine and in several minutes he will come back to resume his speech".
Mubarak is a former air force
But it was about 45 minutes before he reappeared in the amphitheater-like chamber, where the members of parliament had waited in their seats.
Mubarak had postponed to Wednesday the keynote speech he originally planned to deliver to parliament on Sunday after falling ill with a fever.
Every year Mubarak reviews his government's domestic and foreign policy in a speech marking the opening of parliament.
The Egyptian leader was also scheduled to speak to the nation on Thursday on the night which marks the revelation of the Quran to the prophet Muhammad.
It was not clear whether he would keep to that schedule.
A former commander of the air force and vice-president, Mubarak became president of Egypt after the assassination of President Sadat in October 1981.
He was the target of an assassination attempt in Addis Ababa, Ethiopia, in June 1995.