The decision comes two days after twin bombings that hit Egypt's St George Cathedral in Tanta and St Mark's Cathedral in Alexandria on Palm Sunday, killing 46 and injuring more than 120 others during prayer services.
The state of emergency is now in effect following parliament's approval.
According to the Egyptian constitution, any state of emergency must be confirmed in parliament by majority vote within seven days of its declaration by the president.
President al-Sisi in a brief television appearance on Sunday had announced the state of emergency for three months.
Sisi had said a top-level council for fighting terrorism and extremism will also be set up. Before making the announcement, he had called a National Defence Council meet.
The first blast took place in the Coptic church of Mar Girgis, also known as St George, in the Nile delta city of Tanta, about 120 kilometres from Cairo, and killed 27 people and injured 78, according to the Egyptian Health Ministry.
The Islamic State claimed responsibility for the attacks.
Coptic Christians make up about 10 per cent of Egypt's population of 85 million.
Egypt's Christian minority has often been targeted by Islamist militants. In December, a suicide bombing claimed by an IS affiliate killed 29 people during Sunday mass in Cairo.
Egypt has seen a wave of attacks by militants since 2013 when the military toppled president Mohammed Morsi, an elected leader who hailed from the Muslim Brotherhood, and launched a crackdown against Islamists.
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