Dear Pankaj Verma,
If you're a workman, you'll be governed by the Industrial Disputes Act, 1947. In such case, you are required to approach the Labour Commissioner. He may either refer your dispute to the Labour Court or pass orders. If you're not satisfied with his orders, then you yourself may challenge the same before the Labour Court. If you're not a workman, then you'll be relying upon your Employment Agreement and thus, you'll be governed by the Indian Contract Act, 1882. In such case, you may directly approach a Civil Court. You cannot approach a Magistrate for Labour/Employment issues.
email@example.com, Advocate, Chennai.