President Donald Trump is scheduled to attend the museums' opening, a White House official said on Monday, speaking on condition of anonymity to discuss the trip before it is formally announced.
The two men have traded barbs for the better part of the year after Lewis, a high-profile Hillary Clinton supporter, said he didn't see Trump as a "legitimate president" in January.
"President Trump's attendance and his hurtful policies are an insult to the people portrayed in this civil rights museum", they said.
The NAACP has also called on Trump to skip the event.
Earlier this week, Lewis expressed doubts as to whether he could "live with myself" if he was on the program with the president at the ribbon-cutting event in Mississippi.
"The president hopes others will join him in recognizing that the movement was about removing barriers and unifying Americans of all backgrounds", she said.
According to Associated Press, the White House says it is "unfortunate" that congressmen Lewis and Thompson won't be joining President Trump at the opening honoring the "incredible sacrifice civil rights leaders made to right the injustices in our history".
Some said Trump's record on racial issues makes his presence offensive, and plan to protest. "After President Trump departs, we encourage all Mississippians and Americans to visit the historic civil rights museum". "I don't know anyone who thinks this is a smart move".
"Why should I protest something that I worked so hard for?" asked Hezekiah Watkins, 70, who lost count of how many times he was arrested for civil rights protests and at one point even shared a cell with the Rev. Dr. Martin Luther King Jr.
In the 1950s and '60s, segregationist whites waved Confederate flags and slapped defiant bumper stickers on cars declaring MS "the most lied about State in the Union".
Saturday's ceremony will also feature speeches from former NAACP chairman Myrlie Evers and Rep. John Lewis (D-Ga.). The Rev. C.J. Rhodes, a prominent African American clergyman, tweeted Thursday morning that Lewis' "voice is needed here now more than ever".
Reuben Anderson, the first black state Supreme Court justice, has said he won't abandon the platform after helping to lead private fundraising efforts for the museum. A museum of Mississippi History covers 15,000 years of human habitation.
Katie Blount, director of the Mississippi Department of Archives and History, said the department looks forward to celebrating the museum's opening.
According to The Republic, two museums, The Museum of Mississippi History and The Mississippi Civil Rights Museum, will share one building and will not shy away from the perils of the state's history, including slave chains, graphic lynching, firebombing photos and KKK robes.