The prime minister said reconciliation is not just a matter between government and Indigenous people, but must also involve non-government actors as well.
A letter released Tuesday by the president of the Canadian Conference of Catholic Bishops says Pope Francis has not shied away from recognizing injustices faced by Indigenous peoples around the world, but he can't personally apologize for residential schools.
'Obviously I'm disappointed with the Catholic Church's decision not to apologize for their role in residential schools,' said Trudeau.
'Reconciliation is not just between government and Indigenous peoples, it's between non-Indigenous Canadians and Indigenous peoples as well. We will keep working with communities, keep working with individuals on the path to reconciliation because we know taking responsibility for past mistakes and asking forgiveness is something that is core to our values as Canadians.'
A papal apology was one of the 94 recommendations made by the Truth and Reconciliation Commission. During a visit to the Vatican last year, Trudeau personally asked the Pope to consider such a gesture.
The commission recommended an apology similar to that offered by the Pope to Irish victims of sexual abuse in 2010. In 2015, Pope Francis issued an apology in Bolivia to Indigenous peoples in the Americas for the 'grave sins' of colonialism.
In the letter issued Tuesday, Bishop Lionel Gendron, president of the Canadian Conference of Catholic Bishops, says that while 'the Holy Father is aware of the findings of the Truth and Reconciliation Commission' and takes them 'seriously,' he 'felt that he could not personally respond' to the request for an apology.
Gendron writes that the Pope has not ruled out a visit to Canada and a meeting with Indigenous Peoples, but in the meantime is encouraging Canadian bishops to continue working with Indigenous Peoples on reconciliation and projects that help with healing.
Sen. Murray Sinclair, the former head of the Truth and Reconciliation Commission, said a lack of apology could interfere with the healing process.
'I think there's always been a bit of a schism between those Indigenous communities that have members of the Catholic church versus those who are not members of the Catholic church within their communities and I think this is going to add to that tension,' he said.
Canada won't give up on apology: Bennett
Assembly of First Nations National Chief Perry Bellegarde said in a statement he has written to Pope Francis urging him to come to Canada to meet Indigenous peoples. He is also seeking a direct meeting with the Pope to discuss the issue further.
'Hearing an apology directly from Pope Francis would be an important act of healing and reconciliation, much like his apology delivered to the Indigenous peoples of the Americas in 2015,' Bellegarde said.