"We made a mistake," the National Archives, a facility of the National Archives and Records Administration (NARA), said in a statement on Saturday, adding "we are and have always been completely committed to preserving our archival holdings, without alteration."
The statement went further to say the alterations were done because it was not an "archival record," but one licensed to be used as a promotion.
The agency maintains that it does not alter images or documents that are displayed as artifacts.
"Nonetheless, we were wrong to alter the image," the statement said.
The photo -- taken from the first Women's March in Washington back in 2017 -- was used to promote their exhibit "Rightfully Hers: American Women and the Right to Vote," that looks into the 19th Amendment and the women's suffrage movement.
During the president's first full day in office, more than 500,000 participants lined the streets to march for women's rights. The exhibit showed the 2017 image superimposed with another photo representing a women's protest in 1913.
The fourth official Women's March took place on Saturday morning, again a place where participants took to the streets of the nation's capital to protest -- with words and signs often directed at the Trump administration and its perceived threats to women and civil rights.
The 2017 photo, taken by Getty Images' Mario Tama, shows the protesters standing in front of the Capitol building, some holding vulgar or condemnatory signs.
"As a non-partisan, non-political federal agency, we blurred references to the President's name on some posters, so as not to engage in current political controversy," the NARA said in a statement on Friday.
One specific example, first reported by the Washington Post, shows a sign that says "God hates Trump." His name was noticeably altered in the photo and was barely legible. The photo also blurred out several references to female genitalia.
"As a family-friendly museum which hosts many groups of students and young people each day, we also blurred some words that could be perceived by some museum visitors as inappropriate, so as not to distract from the graphic's intended purpose," NARA said. "The decision to do this was made during the exhibit development process by a group that included agency managers and museum staff members."
The National Archives said it has removed the display on Saturday afternoon, adding that it will be replaced with an unaltered image.
"We apologize, and will immediately start a thorough review of our exhibit policies and procedures so that this does not happen again," the statement said.