Gregory Yusuke Shiga, 34, was arrested Monday after a yearlong investigation that involved the FBI.
The fire on April 16, 2011, caused more than $6.5 million in damage. Shiga is accused of breaking into the church's sanctuary late at night to start the blaze. Authorities have not released a motive for the crime.
Prosecutors asked that Shiga's bail be set at $1 million. If convicted, Shiga could face up to 12 years to life in state prison.