The 14-member regional assembly in Nenets autonomous region voted unanimously against recalling Alexander Sabadash, the region's representative to Russia's Federation Council, NTV said.
Prosecutors, meanwhile, searched the offices of the region's governor, Alexei Barinov, the Interfax news agency reported, in what could be a response to the legislators' defiance.
The Prosecutor-General's office in Moscow said in a statement that a criminal case for embezzlement and misuse of budget funds had been opened against the governor, the AP reports.
The Nenets vote and a similar move by provincial lawmakers in the Siberian region of Khakasia earlier this week represented a rare challenge to President Vladimir Putin's government from provincial authorities, who usually toe the Kremlin line.
"Regional legislators are seen as voting-machines. The orders come from above and you vote. There were no reasonable arguments, no discussion," one Nenets lawmaker, Vyacheslav Lysakov, said in comments broadcast on NTV.
The Federation Council's speaker, Sergei Mironov, relieved four upper house members last week in a move broadly interpreted as part of a Kremlin shake up in which several top security and law-enforcement officials also lost their jobs.
Mironov said Friday that Sabadash from Nenets had turned up only infrequently to the senate sessions.
Commentators said that the four house members who lost their jobs might have been linked to a corruption scheme involving senior customs and other law-enforcement officials.
Early in his first term, he initiated legislation that deprived provincial governors of their seats in the upper house and replaced them with regional representatives named by provincial legislatures on the Kremlin's blessing. Putin then abolished the direct election of governors, making them effective Kremlin appointees.
The troops of the Southern and Western military districts will begin to return from Russia's southern borders to the points of their permanent deployment starting April 23