Akhmednabi Akhmednabiev, deputy editor of the Novoe Delo, was killed in his car in the regional capital of Makhachkala, RIA Novosti reported.
His death was "most likely" linked to his work, the Investigative Committee of Russia said in a statement. The committee noted Akhmednabiev had been the target of an assassination attempt in January when someone shot at his car.
Russia is one of the most dangerous places in the world for journalists, the Committee to Protect Journalists said. Since 1992, 55 media workers have been killed in the country, many of them in the North Caucasus region.
The Organization for Security and Co-operation in Europe decried Akhmednabiev's killing.
"This murder is a horrid reminder that much more needs to be done in Russia to ensure and guarantee the safety of journalists," Dunja Mijatovic, the OSCE representative on freedom of the media, said in a statement.