Prime Minister Imran Khan on Thursday thanked Iranian Supreme Leader Ayatollah Ali Khamenei and Turkish President Recep Tayyip Erdogan for speaking up against the "oppression and massacre" of Muslims in India and residents of Indian-occupied Kashmir.

Taking to Twitter, the premier regretted that only a "few voices" from the Muslim world were speaking out to condemn the actions of Indian Prime Minister Narendra Modi's "Hindu supremacist" regime.

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"Sadly, few voices from the Muslim World are speaking out & condemning this; & more voices are being raised in the West condemning the Hindu Supremacist Modi regime's massacre of Muslims in India & Kashmiris in IOJK," he wrote.

The prime minister's statement came in response to a tweet by Khamenei in which he urged India earlier in the day to “confront extremist Hindus” and “stop the massacre of Muslims”, adding to the international fallout over deadly violence targeting Muslims in New Delhi.

At least 44 people were killed and hundreds injured in the worst communal riots in the Indian capital in decades, triggered by clashes between supporters of a new citizenship law and those against it.

“The hearts of Muslims all over the world are grieving over the massacre of Muslims in India,” Khamenei said in a tweet in English, just days after New Delhi rebuked Iran's foreign minister for commenting on the same issue.

"The government of India should confront extremist Hindus & their parties & stop the massacre of Muslims in order to prevent India’s isolation from the world of Islam," he added. The tweet was accompanied by the hashtag #IndianMuslimslnDanger.

“Iran condemns the wave of organised violence against Indian Muslims,” Foreign Minister Mohammad Javad Zarif had tweeted on Monday, in response to which New Delhi summoned the Islamic Republic's ambassador and lodged a protest.

“We do not expect such comments from a country like Iran,” foreign ministry spokesman Raveesh Kumar said in a statement later.

The Citizenship Amendment Act provides non-Muslims from Afghanistan, Bangladesh and Pakistan a fast track to Indian citizenship.

Prime Minister Modi's Hindu nationalist government says this is required to help minorities from those mainly Muslim countries.

Critics argue the law discriminates against Muslims and violates the spirit of India's secular constitution. Hundreds of thousands of people have taken part in protests since December.

Earlier this week, the office of the UN High Commissioner for Human Rights filed an intervention application in the Indian Supreme Court against the citizenship law.