I am working in an Indian IT company which is not a registered company.
Would an experience certificate from such a company be valid or not?
I'm working under the assumption that the law requiring businesses to register is generally followed. In this case your results would completely depend on the party which is using your certificate.
For another small company without well established HR processes or another company in the same area that would be able to confirm the existence of the first without relying on the Ministry for confirmation, you might not run into issues.
For a MNC or very large national company you are much more likely to run into trouble. Organizations of this nature will have processes that attempt to weed out fraud like claiming experience from companies that don't exist.
For any interactions with bureaucracy like government or professional bodies there is potential for extra headaches. Reporting experience towards professional certifications or for eligibility for social assistance programs may prove more difficult.