From the standpoint of many Indian philosophical traditions, the atomistic realism of Vaiśeṣika is seen as both ingenious and deeply problematic. A central difficulty concerns the status of the atoms themselves: if they are truly partless and indivisible, critics ask how they can enter into spatial relations such as contact, and how they can form extended wholes like pots or bodies. If, on the other hand, they have distinguishable sides or parts that allow for such contact, they would no longer be genuinely partless. This tension leads to further questions about the transition from many to one: at what precise point do a plurality of discrete atoms become a single, unified object, and what ontological status does this “whole” have beyond its atomic constituents.

Related to this is the problem of qualities and emergent properties. Vaiśeṣika posits eternal, unchanging atoms as the basic substances, with change explained through their recombination, yet the world of experience is rich with colors, tastes, cognitions, and moral experiences. Critics argue that the theory struggles to show how such qualitative richness can arise from combinations of units that are either qualityless or severely limited in their own qualities. The doctrine that effects are entirely new entities not pre-existent in their causes is also challenged, since it appears to sever the intelligible link between cause and effect and makes the emergence of new wholes seem mysterious. Some schools suggest that what is taken as a new, independent whole is better understood as a conceptual construction rather than an ultimate reality.

Another line of criticism concerns the epistemic and metaphysical status of atoms. Atoms are, by definition, imperceptible and are introduced to explain persistence and change in the world of experience. Opponents question whether such unobservable entities, posited largely to save the appearances, are necessary or parsimonious, especially when other systems appeal instead to momentary events, underlying prakṛti, or non-dual consciousness. There is also unease about the special relation of inherence (samavāya), invoked to connect atoms with composites and with their qualities; this relation is seen by many as a mysterious device introduced solely to hold the system together, and it risks either infinite regress or conceptual emptiness.

Finally, several traditions challenge the broader metaphysical picture that undergirds Vaiśeṣika atomism. Advaita Vedānta regards the entire plurality of atoms and substances as ultimately illusory, an appearance within non-dual Brahman rather than a final description of reality. Buddhist thinkers, emphasizing dependent origination and momentariness, see the postulation of enduring, independent atoms as at odds with the pervasive flux and interdependence disclosed in analysis and meditative insight. There are also questions about how an all-pervasive self can coherently interact with localized atomic aggregates such as the body and sense organs, given the strict categorical distinctions in the Vaiśeṣika scheme. Taken together, these criticisms suggest that while atomism offers a powerful explanatory framework, it may not fully align with either rigorous logical scrutiny or the deepest insights of contemplative experience.