The pontiff said that "avoiding a pregnancy is not an absolute evil"
Pope Francis has suggested women exposed to the Zika virus may be permitted to use artificial contraception.
The virus has been linked to cases of microcephaly, which can leave babies with unusually small heads.
"Abortion is not a lesser evil. It is a crime," said the pontiff in response to a question about how best to combat the outbreak across Latin America.
But he added: "Avoiding a pregnancy is not an absolute evil."
The Pope cited one of his predecessors, Paul VI, who relaxed the Church's rules by authorising nuns working in Africa to use contraceptives due to the high risk of them being raped by soldiers.
His comments veer from statements made by Catholic leaders in the region, who have reiterated the Church's opposition to what it calls "artificial" birth control and abortion.
Instead, Church officials have recommended abstinence or scheduling sexual relations for the least fertile periods of a woman's menstrual cycle.
Abortion is banned or severely restricted in many affected countries.
The United Nations has urged countries hit by the virus - which is spread by the Aedes mosquito - to ensure women have access to contraception to reduce the risk of infection.
The Pope's remarks came as he criticised Republican presidential candidate Donald Trump's views on immigration, saying they are "not Christian".