"A president that has lost his way that badly, that has no ability to see the image of God in these little fellow human beings, if he can't do that right, then he has no place in any station of government and we need to realize that he is an enemy of humanity," Franks said to the "How to Take Back America" conference.
Bethany Haley, spokeswoman for Franks, said the congressman was referring to "unborn humanity" and should have clarified his statement. She also said that Franks meant to say that Obama's abortion-related policies have no place in government, rather than that Obama has no place in government.
Haley said she spoke to Franks early Tuesday before he boarded a plane from Arizona to Washington.
"He was just referring to the way President Obama has set himself up as the most pro-abortion president in America's history," Haley said. She ticked off a list of the president's policies and appointments she said were favorable to abortion rights.
"It's a trend - it's not just one or two things. Ever since his days in the Illinois Senate, President Obama has been radical on the issue of abortion," Haley said.
A White House spokesman had no immediate comment.
A video recording of Franks' speech was provided by the liberal interest group People for the American Way.
Franks' remarks "show a stunning lack of respect for our president and the office of the presidency," said Michael Keegan, president of People for the American Way.
The conference was organized by conservative interest groups, including the Eagle Forum and Faith2Action.
Franks, 52, founded a conservative think, the Arizona Family Research Institute, before his election to Congress in 2002.