So far the investigation has resulted in the arrest or detention of five local Muslim men the government says are tied to terrorism.
Representatives of the Muslim community say methods used by the F-B-I are heavy-handed and in some cases possibly unconstitutional.
Members of mosques in Lodi and Stockton say agents threaten and intimidate interviewees. Marwa Elzankaly, the President of the Bay Area Association of Muslim Lawyers calls the investigation a "fishing expedition".
"Things like threatening them with deportation without knowing what they're immigration status is. Their children being followed around by F-B-I in their cars. F-B-I agents going to their place of employment."
Volunteer attorneys are counseling groups of Muslims on their rights.
The F-B-I won't publicly address specific complaints, but a spokeswoman says investigators are sensitive to the rights and the culture of Muslims. She adds the agency regrets that some people feel uncomfortable with it's methods, but investigators have a job to do.