Citing the lynching of a Muslim man following rumours that he ate beef in Uttar Pradesh's Dadri area, Mr Khan said he was disturbed by a series of incidents against minorities and would urge the UN to take up the matter with the Indian government.
In a letter to UN Secretary General Ban Ki-moon, Mr Khan also attacked RSS accusing it of working to turn secular and pluralistic India into a majoritarian theocratic nation as 'Hindu Rashtra'.
"Facist forces are attempting to create a divide in the society by launching a hate campaign against Muslims and Dadri incident is an example of this," the Uttar Pardesh minister told reporters in Lucknow.
In his letter, the minister said there had been sporadic incidents of ethnic or communal clashes, but the real essence of freedom and secularism has never been under question or threat as it was for last one and half years.
"The new government took oath in the name of Constitution of India, but its motivation, inspiration and guiding light also comes from some other fundamentalist and extra constitutional authority named RSS," he said.
"The government provides tacit support to those campaign or programmes that create fear among minorities and intimidate them," he alleged.
Azam Khan said that to form government in Bihar, Uttar Pradesh and other states, RSS certainly needed an issue on which two communities come face to face.
"After Babri Masjid incident, Dadri was held as it is close to Delhi and the BJP-ruled central government found it easy to use its influence and create tension," he alleged.
"I humbly request to the highest international body to look into our miseries and take care of us and impress upon the Indian government to stick to international agreements and allow to flourish secularism and plurality in the country and not to push the agenda of extra constitutional authorities to turn India into theocratic majority Hindu nation," Mr Khan said.
The minister also said he wanted President Pranab Mukhrjee and PM Modi to call a round table conference and discuss campaign against Muslims in the name of beef and attempts to turn India into a Hindu nation.
Accusing the NDA government of keeping double standard, he said, "They talk something before the world leaders and the UNGA, but do opposite and provide tacit support to RSS and its affiliates to intimidate minorities in the country to convert India into majority Hindu nation."
To a question, he said that narrating his pain before the UN should not be taken as a statement against India. "The UN was constituted to ensure that human rights were not violated in the world and it is viewed equally, therefore I have narrated my pain before it (through the letter)," he said.
A week ago, Mohammad Akhlaq, a resident of Greater Noida, was dragged out of his house after a mob alleged he had killed a cow in his house.