Pope Francis' remarks suggested artificial contraception can be used by women threatened by the Zika virus.
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.
With the song "Las Golondrinas", folklore dancers and dozens of people waving handkerchiefs in farewell, Francis boarded the airplane.
Francis moves around the Vatican in a Ford Focus and tends to stick with economy cars when traveling.
The founder of the shelter for undocumented migrants Hermanos del Camino said that he thinks Pope Francis will change the history of Catholicism with reforms to make it a more open religion and that he will continue to fight corruption in the Vatican.
Mexican Cardinal Norberto Rivera said recently that the pope would arrive Feb. 12, but that date has not been confirmed by the Vatican.
The 'Instrumentum Laboris', a road map for issues to be debated by the assembly, repeated the Church's opposition to gay marriage and to adoption of children by gay people but made no specific reference to the pastoral care of gay couples.
The report 'Better Growth, Better Climate' shows that it is possible to generate economic growth and combat climate change at the same time.