In a Sunday statement condemning Akin's remarks, Romney said his administration would not oppose abortion in cases of rape. That puts him at odds with his party's official line.
Romney is set to be nominated for president at the Republican National Convention that opens Monday.
"The details of some of these things, like an exception for rape or life of the mother, these are not uncommon differences that candidates have and don't share some of the detail on those exceptions," RNC Chairman Reince Priebus said Tuesday on MSNBC. "But as far as our platform is concerned, I mean, this is the platform of the Republican Party. It is not the platform of Mitt Romney."
The party's platform says members of the GOP "assert the sanctity of human life and affirm that the unborn child has a fundamental individual right to life which cannot be infringed. We support a human life amendment to the Constitution."
Romney's position is also at odds with his running mate, Wisconsin Rep. Paul Ryan, who opposes abortion only in instances where the life of the mother is at risk. That's closer in line with the Republican Party's official position.
A Ryan aide downplayed the difference. "He knows he is joining the Romney ticket and the Romney administration will reflect the views of the nominee," Ryan spokesman Michael Steel told reporters traveling with Romney's No. 2 from Pittsburgh to Philadelphia.
Ryan has voted for legislation that has included exceptions for rape, incest, and the life of the mother, another spokesman said.
The decision might have passed with little notice if not for Akin, whose weekend comments drew intense criticism and quick calls for him to step aside.
Romney did not call for Akin to leave the race until about two hours before a state-imposed deadline for him to drop out without going to court. Akin was still in the race at 6 p.m. EDT Tuesday, and now has until Sept. 25 to seek a court order to take his name off the ballot. After that date, there is no way for Akin to leave the race.