"Members run and take positions. It's a personal position, and they have to stake out their own personal position, just as I have," McCarthy said, according to Vice News on Thursday.
His comments came as he pushed back against Alabama's restrictive abortion law that excluded exceptions for rape and incest.
McCarthy's position reflected the personal view of his party's chairwoman, Ronna McDaniel, who told CNN that she would include those exceptions in abortion legislation. McDaniel, however, also said that her party had a broad tent and allowed states like Alabama to craft their own legislation even if it didn't stricly adhere to her position.
State-level abortion initiatives -- in particular, Alabama's and New York's -- have put politicians in both parties in tough spots as they faced questions about aspects of the procedure that were seen as the most difficult to defend.
According to Vice, the Republican Study Committee (RSC), a prominent conservative caucus, circulated a "messaging guidance" email that blamed the media for creating division in the GOP and directed members to use talking points that supported Alabama's law.
"While some Republicans may disagree with the timing and/or particular legal strategies being implemented with the various state measures, it is critical our members speak with clarity and conviction about the broader issue of the sanctity and inherent value of every single human life," the email read.
Claiming that "every single human life has inestimable dignity and inherent value," it argued that rape and incest didn't justify abortions.
"Committing a second violent act with abortion to a woman who has already been victimized by an act of rape or incest could phyiscally or psychologically wound her further," the guidance also argued.
When the president tweeted on the issue, however, he said he supported exceptions for rape, incest, and protecting the mother's life.
"As most people know, and for those who would like to know, I am strongly Pro-Life, with three exceptions - Rape, Incest, and protecting the Life of the mother - the same position taken by [former President] Ronald Reagan," Trump said.
His tweet reflected a vigorously pro-life agenda and Supreme Court nominees who could overturn longstanding precedent on the issue.
Groups like the American Civil Liberties Union (ACLU) have sued over many state laws, including Alabama's, setting up legal challenges for the court to consider. While it's unclear how the Supreme Court will rule on the issue, pro-choice advocates have been adamant about politicians defending abortion access.
But Democrats, like Republicans, seemed to face differences within their own party. Just after Louisiana's Democratic governor signaled he would sign his state's "heartbeat" legislation, the co-chair of the Congressional Progressive Caucus called for "strong primaries" against pro-life Democrats.
While Democratic leaders have indicated it was possible to be pro-life and a Democrat, Senate Minority Leader Chuck Schumer, D-N.Y., previously made clear that his party was pro-choice.