The good news first : you don't need certification from an incubator to be called a startup.
Now the confusing part: you need to apply to the startupIndia site , process how are you different and how will you create employments and then the govt will decide whether you are a startup or not.
An entity shall be considered as a Startup:
a) if it is incorporated as a private limited company (as defined in the Companies Act, 2013) or registered as a partnership firm (registered under section 59 of the Partnership Act, 1932) or a limited liability partnership (under the Limited Liability Partnership Act, 2008) in India; and
b) up to seven years from the date of its incorporation/ registration; however, in the case of Startups
in the biotechnology sector, the period shall be up to ten years from the date of its incorporation/ registration; and
c) if its turnover for any of the financial years since incorporation/ registration has not exceeded Rupees 25 crores; and
d) if it is working towards innovation, development or improvement of products or processes or services, or if it is a scalable business model with a high potential of employment generation or wealth creation.
Provided that any such entity formed by splitting up or reconstruction of a business already in existence shall not be considered a ‘Startup’.
While it's a great way to bring a lot more companies under the purview, having a subjective definition creates favouritism and eventually, a corrupt system.