TANTA, Egypt — Rattling a country already wrestling with a faltering economy and deepening political malaise, two suicide bombings that killed 44 people at Coptic churches in Egypt on Palm Sunday raised the specter of increased sectarian bloodshed led by Islamic State militants.

The attacks constituted one of the deadliest days of violence against Christians in Egypt in decades and presented a challenge to the authority of the country’s leader, President Abdel Fattah el-Sisi, who promptly declared a three-month state of emergency.

Security is the central promise of Mr. Sisi, a strongman leader who returned on Friday from a triumphant visit to the United States, where President Trump hailed him as a bulwark against Islamist violence. Mr. Trump made it clear that he was willing to overlook the record of mass detention, torture and extrajudicial killings during Mr. Sisi’s rule in favor of his ability to combat the Islamic State and defend minority Christians.

On Sunday, Mr. Sisi found himself back on the defensive, deploying troops to protect churches across the country weeks before a planned visit by Pope Francis. Mr. Sisi rushed to assure Christians, who have traditionally been among his most vocal supporters and now fear that he cannot protect them against extremists.