What if I have got a job in the same company where they have Category 1 warning letter in my file?
So I worked as an intern for this MNC, after 2 years of working in another firm, I reapplied and went through interviews and now my offer letter has to be processed in 2 weeks.
I had a warning letter in my file there when I interned, although it's been 2 years but I'm scared that during background check they might withdraw the offer.
Please help me here.

I'm going to assume from context you have a position presently.

If they want a commit from you before they make a commitment to you (which is a bit ridiculous on their part): accept the offer letter, say you need to give 4 weeks notice under contract for your current employer to give yourself padding. Submit your two weeks notice to your current employer after they confirm your offer. Adjust the dates according to what your actual obligations are.

Personally, I won't submit my notice until I have a signed offer in hand that guarantees employment.

@SortOfTested I haven't resigned yet, but after accepting the offer I have to resign. And after that they do background check in which they have right to withdraw if they find something out.