Police in northern India arrested a BJP youth leader for posting anti-Muslim comments on social media, along with 50 other people who took part in sporadic unrest among minority Muslims in parts of India last week over Sharma's remarks.
Suspended BJP spokesperson Nupur Sharma's alleged derogatory remarks on the Prophet during a debate on national television created Sporadic unrest in India.
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Sharma's remarks sparked uproar among Muslims in India and triggered diplomatic protests from Islamic countries demanding an apology from the Indian government.
Sharma has been suspended from the party while another spokesman, Naveen Kumar Jindal, was expelled over comments he made about Islam on social media.
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India tightened public security on Wednesday after the circulation of a letter warning of Islamist militant attacks to avenge derogatory remarks about the Prophet Mohammad by an official of the ruling Hindu nationalist party.
Several Indian media groups shared the June 6 letter attributed to al Qaeda's branch in the Indian subcontinent (AQIS) in which threats were made to carry out suicide bombings in Indian states to defend, it said, the honour of the Prophet.
A federal home ministry official said intelligence agencies were checking the authenticity of the threats issued by AQIS.
"We have also ordered state police to ensure public gatherings or protests are not allowed as they could be targeted by the militant group," a senior home ministry official in New Delhi said.
The new controversy has become a diplomatic challenge for Modi who in recent years has cemented strong relations with energy-rich Islamic nations.
Islamic rights groups in India said that it was the first time influential foreign leaders had spoken out against what they called humiliations experienced by the minority community.
"Our voices have finally been heard, only world leaders can nudge Modi's government and his party to change their attitude towards Muslims," said Ali Asghar Mohammed, who runs a voluntary rights group for Muslims in India's commercial capital Mumbai.
India's foreign ministry said on Monday the offensive tweets and comments did not in any way reflect the government's views.
Instructions have been issued to several senior members of the BJP to be "extremely cautious" when talking about religion on public platforms.