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Flynn told ABC's "This Week" on Sunday that "women have to be able to choose" - before telling Fox News on Monday morning that he considers himself a "pro-life Democrat."
"This is a legal issue," he told Business Insider while promoting "Field of Fight," his new book set to be released on Tuesday. "The Supreme Court decided upon this. This is a legal issue. I'm a guy that's a rule-of-law guy, so this has to be decided, and it was decided, by our court system. So it's a legal issue."
"The more important issue for this country going forward is that, this next election will likely choose Supreme Court justices, maybe two, maybe three, maybe four - some think four, potentially," he continued. "So if people want to change the legal aspects of abortion right now, then they must go vote and get the right president in there - which in my mind is Donald Trump - so we can get the right types of Supreme Court justices to basically change whatever it is that we want to change."
When asked by Business Insider executive editor Brett LoGiurato whether he considers himself to be for or against abortion rights, Flynn declined to take a side.
"At this point in time it's a legal issue," he answered. "So I will respect the law of the land."
During his interview with "This Week," Flynn garnered attention for his comments - which provoked ire from antiabortion-rights conservatives and ran contrary to past statements made by Trump on the issue. At least one group, the Susan B. Anthony List, said that Flynn should be disqualified from consideration.
"Abortion, I think for women, and these are difficult issues, but I think women have to be able to choose - sort of a right of choice," Flynn said.
"But I think that's a difficult legal decision, and I think that women are so important in that decision-making process," he continued. "And they are the ones that have to make that decision because they are the ones who are going to decide to bring up that child or not."
He faced immediate backlash from pro-life groups.
"His pro-abortion position is unacceptable and would undermine the pro-life policy commitments that Mr. Trump has made throughout the campaign," Marjorie Dannenfelser, president of the Susan B. Anthony List, said in a statement.
On Monday's edition of "Fox & Friends," Flynn said that he is a "pro-life Democrat" and added that he believes that "the law should be changed."
"This pro-choice issue is a legal issue that should be decided by the courts," he said. "I believe in law. If people want to change the law, they should vote so that we can appoint pro-life judges. I believe the law should be changed."