When you are required to make electronic payments but pay by other means, CA can assess a penalty equal to one percent of the amount paid, unless your failure to pay electronically was for reasonable cause and not willful neglect.

Effective January 1, 2010: Since passage of the Mandatory e-pay law for Individuals, compliance by taxpayers and their representatives has steadily increased. Therefore, in 2010, CA will again not assess the Mandatory e-pay Penalty.  They will continue to monitor compliance levels to determine the appropriate time to begin implementation of the penalty provision.

For more information about the e-pay law and making your tax payment, go to ftb.ca.gov and search for Mandatory e-pay.

Source:  CA FTB Tax News January 2010