President Kais Saied sparked an outcry this week after saying "hordes" of sub-Saharan African migrants were causing crime and posed a demographic threat in Tunisia.
Saied later sought to reassure "legal" migrants they were welcome but doubled down on claims that those in Tunisia illegally were changing the composition of the country.
In a statement, the AU Commission said it had called Tunisia's representative for an urgent meeting to register "deep shock and concern at the form and substance" of the remarks on behalf of the continent-wide bloc.
"The Chairperson of the African Union Commission H.E. Moussa Faki Mahamat strongly condemns the shocking statement issued by Tunisian authorities targeting fellow Africans which go against the letter and the spirit of our Organization and founding principles," read the statement issued Friday.
Faki said AU member states were obligated "to treat all migrants with dignity, wherever they come from, refrain from racialized hate speech that could bring people to harm, and prioritize their safety and human rights."
Tunisian rights groups accused Saied of hate speech, but the president said those accusing him of racism "want division and discord and seek to damage our relations with our brothers."
Saied, who has seized almost total power since a dramatic July 2021 move against parliament, urged his national security council on Tuesday to take "urgent measures" to tackle irregular migration.
According to official figures quoted by the Tunisian Forum for Social and Economic Rights (FTDES), Tunisia, which has a population of some 12 million, is home to more than 21,000 citizens from sub-Saharan African countries, most of them having arrived in an irregular situation.