I have a few businesses (S corp) in GA. Can GA Dept of Revenue penalize one company for the other company's tax liability?

As with most taxing authorities, they hold far more power than most people may realize. Did they cite you any controlling statute for their position? Compliance with tax laws should always be given the highest priority to avoid such business interruptions. You need to comply with everything they have asked for ASAP. You should consider hiring a tax attorney in your state, also.

Hope this helps.

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