"It is not right to forbid an artist from drawing inspiration from the Holy Scripture," said spokesman Vladimir Legoida, responding to the complaints.
Locals in the Siberian city of Tyumen are demanding the performance of the hit Andrew Lloyd Webber work be cancelled.
Protesters claim it gives an untrue portrayal of Christ and could be blasphemous.
Spokesman Legoida added: "Between blasphemy and non-canonical depictions of the sacred there is a huge gulf which is only invisible to the culturally short-sighted."
The musical has already been cancelled in one Siberian city, Omsk, after similar protests.
Church officials credited the musical with bringing many people to the faith.
