The researcher, who tweets under the pseudonym Elliot Alderson, posted a series of tweets on Saturday stating Mr Modi's app was sending personal user data to a third party.
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Rahul Gandhi, the chief of the the main opposition Congress party, took to Twitter on Sunday to criticise Mr Modi.
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The BJP responded swiftly, saying Mr Gandhi was trying to divert attention.
Last week India's law and IT minister Ravi Shankar Prasad said there were "numerous reports" of the Congress party's connections with controversial data analytics firm Cambridge Analytica.
He asked Mr Gandhi to "explain" the company's role in his social media outreach.
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The party said the data from Mr Modi's app was being used for analytics:
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The security researcher later posted a new tweet on Sunday saying Mr Modi's app had been "quietly" updated its privacy policy.
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