Pope Shenouda III, the patriarch of the Coptic Orthodox Church who led Egypt's Christian minority for 40 years during a time of increasing tensions with Muslims, died Saturday. He was 88.

The state news agency MENA said Shenouda died Saturday after battling liver and lung problems for several years, and a doctor who treated him several years ago said he suffered from prostate cancer that had spread to his lungs. He died at his residence in the main Coptic Cathedral in Cairo, several figures close to the pope said.

"The Coptic Church prays to God that he rest in peace between the arms of saints," a scroll read on a Coptic TV station, CTV, under a picture of the patriarch.

Prime Minister Stephen Harper said he was saddened to hear of Shenouda's death.

"Much beloved and respected leader of the Coptic Orthodox Church, Pope Shenouda III steadfastly led his community through challenging times," Harper said in a statement.

"Pope Shenouda was an exemplary promoter of religious tolerance and understanding, renowned for his humanity and empathy with the Coptic community, as well as people of other faiths. He was cherished by young and old alike, and honoured around the world."

"Baba Shenouda," as he was known to his followers, headed one of the most ancient churches in the world, which traced its founding to St. Mark, who is said to have brought Christianity to Egypt in the 1st Century during the reign of the Roman emperor Nero.

For Egypt's estimated 10 million Coptic Christians, he was a charismatic leader, known for his sense of humour — his smiling portrait was hung in many Coptic homes and shops — and a deeply conservative religious thinker who resisted calls by some Christian liberals for loosening some church rules.

Above all, many Copts saw him as the guardian of their minority living amid a majority Muslim population in this country of more than 80 million people.

Shenouda sought to do so by striking a conservative balance. During the rule of President Hosni Mubarak, he gave strong support to his government, while avoiding pressing Coptic demands too vocally in public to prevent a backlash from Muslim conservatives. In return, Mubarak's regime allowed the Church wide powers among the Christian community.

A sector of Christians — particularly liberals and youth who supported the revolution against Mubarak — grew critical of Shenouda, saying his conservative approach had brought little success in stemming violence and discrimination against their community. Moreover, they argued, the Church's domination over Christians' life further ghettoized the community, making them a sect first, Egyptian citizens second.

Christians have long complained of being treated as second-class citizens, saying they face discrimination in employment and that police generally fail to prosecute those behind anti-Christian attacks.

After Mubarak's fall a year ago, Christians grew increasingly worried over the rising power of Muslim conservatives. Several churches were attacked by mobs, fueled in part by hard-line Islamic clerics who grew bolder in accusations that Christians were seeking to covert Muslim women or even take over the country. Christian anger over the violence was further stoked when troops harshly put down a Christian protest in Cairo, killing 27 people.

In an unprecedented move aimed at showing unity, leaders from the Muslim Brotherhood along with top generals from the ruling military joined Shenouda for services for Orthodox Christmas in January at Cairo's main cathedral.

with files from CBC News