Coptic pope Tawadros II has said that Egypt's Christians feel sidelined.
He said Egypt's Christians feel ignored and neglected by Muslim Brotherhood-led authorities.
Pope Tawadros said that the Egyptian government proffers assurances but have taken little or no action to protect them from violence.
The pope called official accounts of clashes at Cairo's Coptic cathedral on 7 April "a pack of lies".
He also voiced dismay at attempts by President Mohammed Mursi's Islamist allies to purge thousands of judges appointed under ousted President Hosni Mubarak.
He said the judiciary was a pillar of Egyptian society and should not be touched.
The pope said: "There is a sense of marginalisation and rejection, which we can call social isolation."
He said Christians make up at least 15% of Egypt's 84m people and that most Egyptians are Sunni Muslims.
Attacks on churches and sectarian tensions increased significantly after the rise of Islamists to power following the 2011 uprising that overthrew Mubarak, even though Christians had demonstrated alongside Muslims for his removal.
Pope Tawadros, the 118th head of Coptic Orthodox church, was picked on 5 November in a ceremony steeped in the traditions of a community that predates Islam's arrival in Egypt.
He studied pharmacology in Egypt and England and managed a state-owned pharmaceutical factory for a few years before becoming a monk.
The 60-year-old pontiff succeeded Pope Shenouda III, who had led Egyptian Christians for four decades, clashing early on with former President Anwar Sadat but enjoying warmer relations with Mubarak, who acted as the Copts' political protector.
Asked about the government's response to this month's attacks, he said: "It made a bad judgment and it was negligent... I would have expected better security for the place and the people."
Mr Mursi and his ministers tried to mend fences with the 60-year-old Coptic pontiff after the 5 April clashes in the town of El Khusus, north of Cairo, in which four Christians and one Muslim were killed.
Sectarian violence spread to the capital's sprawling St Mark's Cathedral, the pope's headquarters, after the funerals.
Riot police appeared to stand aside during what was the first attack on the seat of Christianity in Egypt in more than 1,400 years.
Coptic churches and community centres have suffered periodic violence for years.
The pope said he was concerned by signs that some Copts were emigrating "because they are fearing the new regime".
Others were going abroad to study, seek work or join family, he said.
Christians have long complained of discrimination in employment.
There are also complaints of treatment by the authorities and called for changes in laws to make it as easy to build or renovate churches as it is for mosques.
The black-robed pontiff, carrying a white-tipped staff and a Coptic cross in his hand, was particularly scathing about an account of the cathedral violence posted on the Facebook page of Mr Mursi's national security adviser, Essam Haddad.
Mr Haddad's office said Christians had instigated the clashes by vandalising cars outside the cathedral during the funeral procession.
He said that firearms and petrol bombs had been used from inside the church compound, provoking the security forces.
Mr Mursi has kept his distance, staying away from Pope Tawadros' inauguration and shunning Coptic Christmas celebrations.
This move by Mr Mursi has been to avoid alienating hardline conservative Salafi Islamists who refuse to recognise Christian holidays.
Mr Mursi offended Copts by setting the date for parliamentary elections on the Coptic Easter holiday.
He then admitted when he changed the polling day after Christian protests that he had been aware of the religious festival.