The Sunday morning fire at the Salman Alfarisi Islamic Center in Corvallis destroyed much of the building's administrative office, the Corvallis Gazette-Times reported.
Mohamed Osman Mohamud, 19, a former Oregon State University student, had attended services at the mosque. He was appearing in court Monday after being arrested in an attempt to detonate a van full of what he thought were explosives near Portland's Pioneer Courthouse Square.
FBI spokeswoman Beth Anne Steele in Portland said the arson fire seemed to be an attempt "to interfere with the civil rights of the members of the church to freely worship."
A Corvallis policeman spotted smoke coming from the Islamic center about 2:15 a.m. Firefighters were able to limit damage to one office, and there were no injuries.
Witnesses said the fire might have started from someone throwing a glass full of a flammable liquid through the window.
The FBI office in Portland offered a $10,000 reward for information on the attack Monday.