Clarkson, 49, was an associate professor in NMSU’s College of Business. He took a leave of absence to serve in the Trump administration in the Interior Department and later launched his campaign for Congress.
The incumbent, Steve Pearce, is not seeking re-election and instead running for governor.
Clarkson alleges racial and religious discrimination because he is a conservative pro-life Christian and a member of the Choctaw tribe.
He said NMSU canceled his leave of absence and fired him in late April after he announced he was running for Congress.
An NMSU spokeswoman said the university does not comment on personnel matters or pending litigation.
“We’re going to be amending the complaint to include retaliatory defamation,” Clarkson said in a phone interview Friday. “They fired me because of my political beliefs. That’s a felony.”