According to a statement from the Vatican, in regard to the role of the church in the 1994 Genocide against Tutsi, Pope Francis expressed his solidarity with the victims and with those who continue to suffer the consequences of those tragic events.
The Vatican and Pope Francis issued a statement on the meeting. An apology was also sought for the fact that many killings actually took place in Catholic churches.
In an extraordinary statement after Francis' meeting with Rwandan President Paul Kagame, the Vatican acknowledged that the church itself bore blame, as well as some Catholic priests and nuns who "succumbed to hatred and violence, betraying their own evangelical mission" by participating in the genocide.
The church became implicated in 100-day genocide when several of its officials were found to have helped aid and plan the programme of ethnic-cleansing led by extremist Hutus against Tutsis and moderate Hutus.
Other individual priests have since been convicted of human rights violations for heinous acts during the genocide such as bulldozing a church with 2,000 Tutsis inside and raping Tutsi women.
An estimated 5,000 people were killed at the Ntarama Catholic church on 15 August 1994: the site is now one of six major memorials in Rwanda.
Another, Father Wenceslas Munyeshyaka, helped draw up lists of people to be killed and raped young women, according to charges issued by the UN's worldwide criminal tribunal for Rwanda in 2005.
In President Kagame's 25-minute private meeting with the pope, as well as during his meeting with Cardinal Pietro Parolin, Vatican secretary of state, note was made of "the collaboration between the state and the local church in the work of national reconciliation and in the consolidation of peace for the benefit of the whole nation", the Vatican said.
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Amid continued pressure from the government, Rwanda's Catholic bishops a year ago apologized for "all the wrongs the church committed".
"I don't understand why the pope would apologize for sexual offences, whether it is in the US, Ireland or Australia, but can not apologise for the role of the church in the genocide that happened here", Mr Kagame said at the time.
"This stance was easily interpreted by ordinary Christians as an implicit endorsement of the killings, as was the close association of church leaders with the leaders of the genocide", it said.
Rwanda's foreign minister, Louise Mushikiwabo, who accompanied the president on his visit to Rome and to meet with Pope Francis, felt pleased with the meeting and saw it as a positive step moving forward.
Amid continued pressure from the government, Rwanda's Catholic bishops a year ago apologised for "all the wrongs the church committed".
The population of Rwanda, a former Belgian colony, is overwhelmingly Christian, with similar numbers of Roman Catholics and Protestants.
About half of Rwandans are Catholic, but since the genocide many have turned to pentecostal churches.