Police in Bangalore raided the apartment of Mehdi Masroor Biswas in an upscale suburb of Bangalore early on Saturday and seized his mobile phone, laptop and other documents.
Biswas is alleged to be the author of ShamiWitness, which had 17,700 followers, including many foreigners fighting for the Islamic State group in Syria and Iraq, until it was shut down following a report by Britain's Channel 4 News on Thursday.
Tweets from ShamiWitness contained jihadist propaganda as well as information for would-be recruits and messages praising fallen fighters as martyrs.
"He has confessed to the fact that he was operating Shami Witness Twitter account for the last many years ... he used to work in the office in the day and became active on the internet late at night," police director-general LR Pachuau told reporters.
India's moderate population of 150 million Muslims have not often been drawn into sectarian conflicts in the Middle East and elsewhere.
However, an Indian student was recently charged with terrorism-related offences after he returned home from Iraq, where he is alleged to have worked for jihadists.
Biswas's arrest has further fuelled fears that IS militants are attempting to recruit radicalised Muslim youngsters online.
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