When the First Chechen War broke out in 1994, Alkhanov supported the Russian side against the separatists. He was decorated with the Order of Courage for his actions during the separatists' assault on Grozny in 1996. In April 2003, he was appointed Interior Minister of Chechnya in the government of Akhmad Kadyrov and was made a Major General of the Chechen police. When Kadyrov was assassinated on May 9, 2004, Akhnanov became the favoured candidate of the Russian government.