The Brazilian filmmaker, who is responsible for films such as City Of God and The Constant Gardener, said an earlier cut of The Two Popes originally contained more scenes about the topic.
Arriving at the movie's premiere at the BFI London Film Festival, he told the PA news agency: "Of course we tackle these issues, because we couldn't make a film on the church without tackling it, but we had more scenes on child abuse that we cut from the film because we had too much.
"That is what we felt when we first cut the film, if we talked too much about it, it becomes the film, because it's such a topic.
"And that was not the film, this film was really about tolerance, tradition and a spiritual issue, a political issue, and we don't want it to all become about sexual abuse.
"So we tackle it but we don't go thick because it would steal the whole film, it would be a film about it."
Meirelles added he had little interest in the Catholic Church before he made the film, which stars Sir Anthony Hopkins and Jonathan Pryce, saying: "I knew nothing about what was happening and I had no interest at all about the relationship but I like Pope Francis very much, that is what dragged me to the story.
"For the film I think the relationship between both of them is the most interesting part of the film because they don't agree on anything, they really think in opposite ways but they have to find a common ground.
"So the story is about two persons who really don't like each other and having to deal with each other, which is something that is happening in the world.
"Nowadays we tend to hate people who we disagree with and the film is about tolerance, about listening before you hate, listen before you shoot, that is the message that I like in the film."
The director also said that his two stars were as different as the men they play in the way they prepared for the film.
He said: "Tony Hopkins, to prepare himself he reads the lines, for five months he asks us not to change the lines and he studies the part like intellectual, like an academic would do, word by word and the meaning.
"Tony is a classical musician while Jonathan is more jazz, he tries to get the feeling of the pope and how he walks and how he feels and then he can improvise, it's very different approach to characters but working together, for both of them it worked, the jazz and the classical actors, it was amazing."
The Two Popes will be released on Netflix in December.
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