Testing under what conditions a product satisfies the desired properties is a fundamental problem in manufacturing industry. If the condition and the property are respectively regarded as the input and the output of a black-box function, this task can be interpreted as the problem called level set estimation (LSE): the problem of identifying input regions such that the function value is above (or below) a threshold. Although various methods for LSE problems have been developed, many issues remain to be solved for their practical use. As one of such issues, we consider the case where the input conditions cannot be controlled precisely—LSE problems under input uncertainty. We introduce a basic framework for handling input uncertainty in LSE problems and then propose efficient methods with proper theoretical guarantees. The proposed methods and theories can be generally applied to a variety of challenges related to LSE under input uncertainty such as cost-dependent input uncertainties and unknown input uncertainties. We apply the proposed methods to artificial and real data to demonstrate their applicability and effectiveness.