The RMD distribution amount itself is subject to California income taxes as well as Federal taxes, but the penalty (which is actually an additional tax or excise tax) is only at the Federal level. Your federal return is included when the California return is transmitted and California doesn't have a separate form.
You may be able to get the penalty waived if you missed taking your RMD due to an error by the financial institution. You'll calculate that penalty in Part 9 of Form 5329. To request a waiver, enter “RC” (for reasonable cause) and the amount of shortfall you want to be waived on the dotted line next to Line 54.
The IRS will match Form 1099-R with the information reported on the tax return for the year the form is filed with them.
See this tax tips article for more information about Form 5329.
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