Like other Arab leaders, Mr. Mubarak made a point of protecting minority groups to nurture loyal constituencies and patronage systems that he could leverage against his Islamist rivals. Though secular tension sometimes turned violent during his 30 years in power, it was generally contained by the state security apparatus.

Since Mr. Mubarak’s overthrow, however, attacks on Copts and their institutions have been widely reported. In October 2011, for example, following the burning of a Coptic church in Upper Egypt, security forces clashed with Christian protesters: 28 people, mostly Copts, were killed. Last month, Muslim extremists laid siege to Egypt’s main Coptic Cathedral in Cairo. The assault, which according to witnesses and video footage the police did little to prevent, followed a funeral for five men who died days earlier, in Khusus, a small town north of Cairo, in clashes with militants.

Critics blame President Mohamed Morsi and his government for failing to quell the violence. In an editorial last month, the state-owned Al-Ahram Weekly called the killings at Khusus “a symptom of irresponsibility in high places, of indifference that can lead the state to the verge of collapse,” while the Copts’ spiritual leader, Pope Tawadros II, accused Mr. Morsi of “delinquency” and “misjudgments.”

Mr. Morsi, a longstanding member of the Muslim Brotherhood who resigned from the group before taking office, issued a statement of regret following the attacks that struck many observers as perfunctory. Last week, he pointedly sent a low-level functionary as his representative to the Easter Mass led by the pope.

Mingled with the threat of physical violence is the fear among Coptic business leaders that they are being singled out for punitive enforcement of the tax code.

Orascom Construction Industries, the flagship in the Sawiris family business group and the largest publicly traded Egyptian company, is alleged by the finance minister to have failed to pay taxes on profit realized from its 2007 sale of a cement unit to the French cement maker Lafarge. The charge confounded analysts; Egypt has no capital gains tax, they point out, and O.C.I. took the cement company public two months before its sale precisely to benefit from tax incentives aimed at encouraging companies to list their shares.

Still, in April, O.C.I. announced that it would pay 7 billion Egyptian pounds, or $1 billion, to Cairo’s tax authority and prosecutors promptly lifted a travel ban on the company’s chairman, Nassef Sawiris, and his father, Onsi. O.C.I., meanwhile, is pursuing plans announced in January for a share swap with its Dutch unit, OCI NV, which would effectively shift trading in the company’s stock to Amsterdam.