Pope Francis compared having an abortion to avoid birth defects to the Nazi era idea of trying to create a pure race.
Speaking to a delegation of Italy's Family Association in Rome on Saturday, he also reiterated the Roman Catholic belief that a true human family is comprised of a man and woman.
The off-the-cuff comments were confirmed by the Vatican after the meeting.
"I have heard that it's fashionable, or at least usual, that when in the first months of pregnancy they do studies to see if the child is healthy or has something, the first offer is: let's send it away," Pope Francis was reported as saying.
"I say this with pain. In the last century the whole world was scandalized about what the Nazis did to purify the race. Today we do the same, but now with white gloves."
The Nazi quest for a pure race by only allowing healthy children to be born was known as Nazi eugenics. It included abortion and the sterilization of people with physical and mental illness.
In addition to his comments on abortion and fetal testing, Pope Francis made clear what he believes the definition of a human family should be.
"Today, it is hard to say this, we speak of 'diversified' families: different types of families. It is true that the word 'family' is an analogical word, because we speak of the 'family' of stars, 'family' of trees, 'family' of animals ... it is an analogical word. But the human family in the image of God, man and woman, is the only one. It is the only one. A man and woman can be non-believers: but if they love each other and unite in marriage, they are in the image of God even if they don't believe," the Pope said.
His comments come after Argentina, his home country, voted in favor of a bill that would legalize abortion as early as 14 weeks of pregnancy and ahead of his trip to Ireland in August for the World Meeting of Families.