The Vedomosti business daily, citing a source in the local presidential staff, had said Murtaza Rakhimov, who has led the republic since 1993 and whose term expires in 2011, would step down later this week.
The 75-year-old leader's press service said in a statement: "President Murtaza Rakhimov will continue performing his duties as head of the region until his term expires in 2011."
Russian President Dmitry Medvedev has the power to dismiss regional leaders. Vedomosti cited Kremlin sources as saying the recent removal of a local company from Rakhimov's control was a step towards a change of power in the republic.
However, a press secretary for the Bashkir president said: "All talk about Bashkir President Murtaza Rakhimov's early resignation is just rumors and speculation - nothing more."
He said that despite the ongoing financial crisis, economic and social stability has remained in Bashkortostan, and it would be "illogical" to have a leadership change.
Rudik Iskuzhin, a member of the upper house of the Bashkir parliament, described by Vedomosti as one of Rakhimov's likely successors, said he could not confirm the resignation reports.
"The source mentioned by the newspaper is unknown to me. It's difficult to comment on something you know nothing about," he said.