Envoy Ali Chegeni was told that Iran's foreign minister "commented on a matter which is purely internal to India," sources told the Press Trust of India.
Condemning the communal violence, Iranian Foreign Minister Javad Zarif had urged Indian authorities to "ensure the well being of all Indians and not let senseless thuggery prevail".
"Path forward lies in peaceful dialogue and rule of law," he tweeted on Monday.
Besides 47 fatalities, shops, schools and homes were burnt as thugs terrorized northeast Delhi residents for four days before Delhi Police, criticised for their slow reaction, managed to get things under control.
PM Imran likens Delhi ‘pogrom’ to Kristallnacht
The riots, which occurred during a two-day visit by US President Donald Trump, have triggered mass condemnation.
The Organisation of Islamic Cooperation has called on the Indian government to stop “anti-Muslim violence” and the desecration of Islamic places of worship in the country.
The trigger to the violence was allegedly a hate speech by a local politician of the ruling Bharatiya Janata Party against peaceful protesters disapproving India’s new citizenship law.
The controversial legislation grants citizenship to non-Muslim migrants from three neighbouring countries.
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