The top Coptic cleric has withdrawn to a desert monastery to draw attention to grievances among Egyptian Christians.
Pope Shenouda is spiritual leader to millions of Copts
Pope Shenouda III went into retreat at Anba Bishoy monastery in Wadi Natrun on 8 December, but his whereabouts were initially kept secret.
Tensions flared during the last three weeks over fears that Christians were being forced to convert to Islam.
At least 34 Copts were arrested during a demonstration in Cairo and sectarian violence also erupted in Upper Egypt.
"The seclusion of His Holiness the Pope will continue until he reaches a solution [with the government] that satisfies his conscience to the problems related to the Copts," the pope's secretary Bishop Armia told Reuters news agency.
Other Church sources have been quoted as saying he will not resume his duties until the authorities release those people arrested in Cairo.
The generally calm relations between the authorities and the Coptic minority - which makes up 5-10% of Egypt's population - became strained over the case of priest's wife Wafa Constantine.
Government officials had said Mrs Constantine, 48, wanted to convert to Islam but was being prevented from doing so by her family.
Rumours that she had been abducted and forced to convert began circulating among Copts, sparking angry protests outside Cairo's St Mark's cathedral.
Coptic demonstrations in Cairo led to numerous arrests
A number of police and worshippers were injured in protests where stones were allegedly thrown and arrests were made at demonstrations deemed illegal.
The clashes and a sit-in at the cathedral ended when protesters were told that Mrs Constantine was back under the Church's protection.
"The patriarch granted her his mercy and assured her that she remained in the Church," the pope's office said.
Last Thursday, Egypt's prosecutor-general said that Mrs Constantine had gone to police saying she wanted to change her religion, but had decided to remain a Christian after meeting Church officials.
Also this month, police said they had arrested 25 people after sectarian violence erupted in the Upper Egyptian village of Munqateen.
Police were reported to be keeping Muslims and Christians apart after three Christian-owned shops were set ablaze, Christian homes were stoned and police cars were wrecked.
Copts remained the majority in Egypt for centuries after the 7th Century conquest of the country by Muslim armies.
In the modern age, they complain of discrimination, restrictions on church construction and periodic fears that Christians are being forced to convert by Islamic extremists.