The Indian Ministry of External Affairs summoned Ali Chegeni, the Iranian ambassador to India on Tuesday.
The ministry lodged a strong protest over the Iranian Foreign Minister Javad Zarif's criticism of the communal violence in New Delhi, reports the Hindustan Times.
Ali Chegeni was informed that Zarif's remarks, made in a tweet on Monday, amounted to interference in India's internal affairs, said people familiar with developments.
External affairs ministry spokesperson Raveesh Kumar said Chegeni was summoned and a "strong protest was lodged against the unwarranted remarks made by the Iranian foreign minister".
He added, "It was conveyed that his [Zarif's] selective and tendentious characterisation of recent events in Delhi are not acceptable. We do not expect such comments from a country like Iran."
The recent sectarian violence in parts of northeast New Delhi claimed more than 40 lives and injured hundreds. There was also widespread destruction of property.
Protest against Zarif's remarks was in line with India's prickly response to criticism of other issues such as the changes in Jammu and Kashmir last year and the controversial citizenship law. In his tweet, Zarif had said that Iran "condemns the wave of organized violence against Indian Muslims".
He added: "For centuries, Iran has been a friend of India. We urge Indian authorities to ensure the wellbeing of ALL Indians & not let senseless thuggery prevail."
"Path forward lies in peaceful dialogue and rule of law."
Ties between India and Iran have been hit since New Delhi stopped all imports of Iranian crude last June due to the impact of US secondary sanctions. Until then, Iran had been among India's top three energy suppliers.
The two sides have continued to cooperate on the development of the strategic Chabahar port, which is key to India's plans to access Afghanistan and Central Asian states while bypassing Pakistan. However, the Iranian side has continued to call for work to develop Chabahar and an associated railway link to the Afghan border to be expedited.
Iran was the second Muslim-majority country to express concern over the violence in New Delhi. Last week, India's envoy to Indonesia was called in by the foreign ministry to discuss the issue, and the country's religious affairs ministry too expressed concern at the matter.