"Abortion, I think for women, these are difficult issues," he told ABC's Martha Raddatz on "This Week." "I think that's a difficult legal decision, and I think that women are so important in that decision-making process. They are the ones that have to make the decision because they are the ones that will decide to bring up that child or not."
His comments highlight potential friction with delegates at the upcoming Republican National Convention in Cleveland, which will need to ratify Trump's vice presidential choice. Other potential running mates for Trump, each with significant political experience, hew to the party line on abortion.
Flynn is a somewhat political unknown, having never run for or held public office.
Flynn's comment's quickly drew criticism from a prominent anti-abortion group.
"General Flynn has disqualified himself from consideration as Vice President," Marjorie Dannenfelser, president of the Susan B. Anthony List, said in a statement Sunday. "His pro-abortion position is unacceptable and would undermine the pro-life policy commitments that Mr. Trump has made throughout the campaign."
Flynn capped his Army career as director of the Defense Intelligence Agency in the Obama administration for two years. He left in 2014 amid clashes with top intelligence officials and has since become a strong critic of the Obama administration approach to counterterrorism issues.
Asked on Sunday about another prominent social issue, same-sex marriage, Flynn was more coy. "I'm about national security," he demurred.
Flynn's views on immigration, though, do seem to line up with Trump's. The Republican candidate has pledged frequently to build a wall along the U.S.-Mexico border and deport people who have entered the country illegally.
"If it's illegal, it's illegal," Flynn said. "If they're here illegally, then it's illegal. Back to my very first point, the rule of law in this country is probably the single biggest strategic advantage we have. We cannot allow the rule of law to break down."
Flynn also slammed the decision by FBI Director James Comey to recommend not prosecuting Hillary Clinton
over use of her private email server while secretary of state. Attorney General Loretta Lynch has since formally ratified that recommendation.
"Unbelievable," he said. "I mean, the FBI director said that she lied, essentially. What he should not have done is he should not have offered his opinion outside of telling the attorney general. He should not have offered that opinion."
Asked whether he is being vetted by Trump's campaign, Flynn said, "I don't know."
"I have said that service to this country is an honor. I am honored to even be in this discussion," he said. "For a kid from a little town from the smallest state in the union, Rhode Island, it's a pretty big deal ... if people are serious about it, I'll be serious about it."
He addressed why he has remained a registered Democrat, but didn't say whether he'd changed his affiliation.
"I grew up as a Democrat in a very strong Democratic family, but I will tell you that Democratic party that exists in this country is not the Democratic Party that I grew up around in my upbringing," he said. "I vote for leaders."