I recently found out that as an H1B I'm subject to FICA taxes. When I got my H1B visa, I told my employer to please confirm if I had to pay those taxes or not. On the next paycheck they stopped deducting them. Is the employer responsible for any back taxes for 2009? For the IRS to question them, do I first need to get audited?

Thanks,

Yes, H1-B income is subject to FICA taxes and income taxes. Ask employer to start deducting these taxes.

They are aware of it but haven't deducted the FICA taxes yet. How can the IRS find out of this situation? Would they be able to find out only if they ran an audit on me? I work for a company with 300k+ employees, in case that matters.

Looking forward for your answer Mukata.

I don't have answer to your question.
If IRS contacts your employer, then must pay the due FICA taxes and collect it from you.