Alexander Litvinenko died in London of radioactive poisoning on November 23, 2006. British investigators accused agent-turned-businessman Lugovoi of the murder, and demanded his extradition, sparking a major diplomatic row.
The Nezavisimaya Gazeta newspaper cited analysts as saying a change in the party's leadership is likely due to President Dmitry Medvedev's recent announcement that the terms of Russian political parties' leaders may be reduced.
Zhirinovsky named Lugovoi as number two on the party list in September 2007, two months before the parliamentary elections.
On Tuesday the supreme council of the LDPR appointed Lugovoi as the party's supervisor in Russia's Far Eastern Primorye Territory, the Kamchatka Territory and the Irkutsk Region.
The LDPR is the third largest party in the State Duma after United Russia and the Communist Party.