The dismissal of Alu Alkhanov came after days of speculation that he was engaged in a power struggle with Kadyrov, who is alleged by human rights groups to be responsible for abductions and detention of civilians and suspected separatist rebels.
Kadyrov is the son of the late Akhmad Kadyrov, who became Chechen president in 2003 in a Kremlin-conducted election aimed at undermining the separatist rebel movement and who was assassinated seven months later.
Chechnya has been plagued by fighting with separatist rebels for most the past dozen years. A 20-month war ended in 1996 with the withdrawal of Russian troops after rebels fought them to a standstill. The region became de-facto independent and increasingly under the influence of fundamentalist Islam.
In September 1999, Russian forces swept back into the region following an incursion by Chechnya-based fighters into neighboring Dagestan and after fatal apartment bombings in other parts of Russia which officials blamed on the separatists.
Major fighting in the latter campaign died down by 2001, but rebels and Russian soldiers still clash in skirmishes and rebels have continued to bloody Russian forces with roadside bombs and booby-traps.
The fighting left much of Chechnya, particularly the capital Grozny, a moonscape of ruins, but Kadyrov has led a largely federally-funded campaign to rebuild.
He has also cultivated wide personal visibility, including banners that praise him draping buildings, and Alkhanov this week strongly criticized the practice.
"Building a personality cult and idealizing one person will bring no good to our republic and society," he said Monday.
Kadyrov heads a security corps that is widely alleged to abduct and abuse suspected rebels and civilians believed to be connected to them.
After the murder in October of journalist Anna Politkovskaya, who had reported critically on Chechnya, speculation rose that the killing was connected with her investigation of Kadyrov's administration.
Kadyrov denied any connection, saying "I don't kill women."