Union Government
(1) If any question arises as to whether a member of either House has become subject to any disqualification under Article 102(1), the question is referred to the President for decision, and the President's decision is final. (2) Before deciding, the President shall obtain the opinion of the Election Commission and act according to that opinion.
If there's a dispute about whether a sitting MP has become disqualified (for example, secretly acquired foreign citizenship), that question is decided by the President - but only after getting, and following, the Election Commission's opinion on the matter. Note this is a different process from Tenth Schedule anti-defection disqualifications, which the presiding officer (Speaker/Chairman) decides.
If it emerges that a sitting MP has quietly taken up foreign citizenship, a question can be raised and referred to the President, who must seek the Election Commission's opinion before making a final, binding decision on whether that MP is disqualified.