The red notice for Keita, himself a former influential lawmaker, was issued at the request of an investigating magistrate in the Malian capital Bamako, said a source close to the case speaking on condition of anonymity.
News of the warrant was confirmed by a source inside Interpol's Mali office, who also spoke on condition of anonymity.
Keita has lived in Abidjan, Ivory Coast, since the military coup that overthrew his father in August 2020.
Investigative journalist Birama Toure had been working for the Bamako weekly Le Sphinx in the months before his disappearance.
He has not been seen since January 29, 2016, according to his family and the director of the magazine, Adama Drame.
Drame said Toure had been working on a story that would have damaged Keita's reputation and had approached him about it when he disappeared.
Drame and Toure's family suspect he was abducted, tortured and killed after several months in detention.
Keita himself has always denied any role in Toure's disappearance and in 2019 filed a defamation action against the director of the magazine and a radio journalist over the allegations.
The courts in Mali threw out the case for technical reasons, but Drame himself, fearing for his safety, is now exiled in France.
For many Malians, Karim Keita personified what they say was the corruption at the heart of his father's regime.
He escaped arrest by the military when they overthrew his father on August 18, 2020, appearing in Ivory Coast a few days later.
