25% is the subject and population the object of the preposition of.
Fractions and portions can be singular or plural depending of the object of the preposition following.
In the sentence, population is the object of the preposition of. The question is that population is a collective noun and singular, although sometimes functioning as plural (for instance, when referring to all the persons inhabiting a country or region).
Collective nouns can be either singular or plural depending on the verb used by the author to refer to a singular entity or a plurality of members.
In this case, there is no such a specification, so I consider that up to 90% of Indian population suffers from Vitamin D deficiency.