Lisitsyn, 59, was re-elected with 42 votes out of 45, the local legislature's press secretary said.
More than 50% of the members of a local legislature must approve a nominee in order for the candidate to become a regional leader under a Putin-proposed 2004 law that abolished gubernatorial elections and gave the president the right to nominate candidates.
Rights groups in Russia and abroad have criticized the law as undemocratic.
Some regional leaders turn to the Russian president even before the end of their terms, asking him to recommend them to local parliaments in line with the new scheme, which is what apparently happened in this case.
Lisitsyn was appointed head of the regional administration in 1992. He was elected regional governor in 1995, and re-elected in 1999 and in December 2003.