Kris Kobach led restrictive voting initiatives that targeted minorities and perpetuated voter suppression, the not-for-profit legal advocacy group said.
Mr Trump signed an executive order establishing the commission to review alleged voter fraud and voter suppression in the American election system.
Vice President Mike Pence and Mr Kobach, the Kansas Secretary of State, will serve as Chair and Vice Chair of the commission that will "review policies and practices that enhance or undermine the American people's confidence in the integrity of federal elections and provide the president with a report that identifies system vulnerabilities that lead to improper registrations and voting."
After the 2016 election, Trump claimed widespread voter fraud explained why Hillary Clinton emerged with nearly 3 million more popular votes. To date, neither Trump nor his team has provided evidence to substantiate the claims, but they have promised an investigation.
Mr Kobach has been a faithful supporter of Mr Trump’s election fraud claims. In April, he announced the first conviction of a non-citizen voting in the state of Kansas in the 2016 election.
However, the ACLU filed a freedom of information request to challenge the basis for the White House’s voter fraud claims.
ACLU’s Voting Rights Project director said: “President Trump is attempting to spread his own fake news about election integrity. Such claims have been widely debunked, but he is still trying to push his false reality on the American public.
“It is telling that the president’s choice to co-lead the commission is none other than Kris Kobach, one of the worst offenders of voter suppression in the nation today. If the Trump administration really cares about election integrity, it will divulge its supposed evidence before embarking on this commission boondoggle.”
The commission is expected to produce its first report sometime next year.
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