During the 2003 Bashkortostan presidential elections, opposition candidates allegedly found a printing house which consisted of false ballots, which were ordered by Khabirov.

[4][5] Vladimir Korostylev, deputy prosecutor of Bashkortostan, made a statement about the involvement of Khabirov in fake ballot blanks printing, but Florid Baykov, republic's prosecutor, disavowed the statement of his deputy, and the presidential administration designated the incident as a rude provocation of the head's of the republic opponents.

[9] After the appointment of Khabirov as the head of the region, the republic transferred Mount Kushtau to the development of the Bashkir soda company.

On 6 August, a member of the Human Rights Council under the Head of Bashkortostan Elza Maulimshina said that police detained several activists.

[12] On 16 August, Khabirov called for an end in the Kushtau development, stating that the work would remain on pause until a compromise was found.

[13] In July 1993, Khabirov signed the Natural memorial zones of national importance creation decree,[14] which included Kushtau in its list.

[15] Following the arrest of an environmental activist Fail Alsynov and subsequent protests, Khabirov accused separatists of "stoking unrest".

[16] In 2023, the Head of Bashkortostan, Radiy Khabirov, asked deputies of the local parliament to submit a bill to the State Duma proposing to transfer to Russian regions the authority to issue licenses for the extraction of gold using the loose method, worrying about the ecology and health of the region’s residents.

[21] Previously, Khabirov was included by the FBK in the list of corrupt officials and warmongers, with a proposal to impose international sanctions against him.

He was also responsible for organizing a logistics warehouse in occupied Ukrainian territory and opposed anti-war political opposition in Russia.