The pope also strongly upheld the church's opposition to same-sex marriage.
An editorial published Sunday on a website of the archdiocese of Mexico City denied local bishops were out of touch with the people, and added the pope's comments "might be due to someone near him who gave him bad advice."
Francis said that "the commandment 'do not kill' holds absolute value and applies to both the innocent and the guilty."
Pope Francis' remarks suggested artificial contraception can be used by women threatened by the Zika virus.
Francis said that a person who advocates building walls is "not Christian."
The Republican presidential hopeful said that he does not like to fight with the pope.
The crisis is putting pressure on Church doctrine that bans all forms of contraception, and has even stoked a debate over abortion in many conservative Latin American nations.
Francis spoke about the church's handling of sex abuse cases while flying home Wednesday from Mexico.
The former Florida governor said he supports walls and fencing "where it's appropriate" along with other forms of border security measures such as drone aircraft monitoring.
The Republican senator previously favored a pathway to citizenship for immigrants in the country illegally, but now says border security - including expanding the Mexican border wall - is the priority.