Pope Francis has called on warring factions in the Central African Republic to lay down their weapons and instead to arm themselves "with justice, love, mercy and authentic peace."

The Pope took one of the biggest security risk of his papacy when he delivered a message of peace and reconciliation at a mosque under siege from armed Christian militias the capital of Central African Republic, Bangui.

Francis was welcomed to the mosque by the Grand Imam Nehedi Tidjani, along with four other imams, who accompanied him to the podium on the final day of his six-day visit to Kenya, Uganda and the conflict-ridden Central African Republic.

The Pope removed his shoes on entering the mosque.

In his address inside the Muslim PK5 area, Pope Francis recalled the recent violence which has rocked the country, saying "Christians and Muslims are brothers and sisters."

Travelling in his modest popemobile, a light utility vehicle, the Pope was under heavy guard by U.N. peacekeepers and Vatican security.

"We are well aware that the recent events and acts of violence which have shaken your country were not grounded in properly religious motives," said the Argentine pontiff.

"Those who claim to believe in God must also be men and women of peace. Christians, Muslims and members of the traditional religions have lived together in peace for many years.

"Together, we must say no to hatred, no to revenge and no to violence, particularly that violence which is perpetrated in the name of a religion or of God himself. God is peace, God salam."

Before CAR's civil war erupted in March 2013, the Muslim population of the capital said to be some 122,000 but most fled.

Thousands of people gathered at the roadside, cheering as the papal entourage drove down red dirt roads.

The visit by Pope Francis to Bangui was the first time the pontiff has visited an active war zone.

The one time French colony became engulfed in a war after President François Bozizé was ousted in a 2013 coup by Muslim rebels.

In Uganda, the Pope celebrated Mass in front of  hundreds of thousands of people, and spoke at a Catholic shrine dedicated to Christians martyred for their faith in the 19th Century.

On Nov. 27, the Pope addressed an audience of young people in the Kenyan capital, Nairobi, urging them to unite and take a stand against the destructive effects of tribalism and corruption.