Prime Minister Manmohan Singh Monday warned against attempts to derail India's secular values by redefining secularism as a minister called for quotas for minorities.
Addressing the annual conference of state minority commissions here, the prime minister said both majority and minority communities should work together to maintain harmony.
Minority Affairs Minister K. Rehman Khan meanwhile said the government was considering the Ranganath Misra Commission report on reservations for minorities.
Manmohan Singh warned against those who "work against India's secular thought by attempting to redefine secularism".
"To maintain communal harmony, both majority communities and minorities have to work together to create an atmosphere of acceptance and harmony.
"In most parts of the country, the relationship between the majority and minority communities is harmonious although there have been instances where this relationship has been put to severe test, especially of late.
"These aberrations tarnish the image of our country and our society. They cause pain and suffering to the affected people," he said.
The communal riots in Muzaffarnagar in Uttar Pradesh last year left more than 60 people dead and left thousands homeless.
He stressed that pluralism is the keystone of India's civilization and culture and religious harmony, not mere tolerance, is the bedrock of India's secularism.
Manmohan Singh said his government had set up many institutions to "ensure that minorities should not only be provided adequate safeguards but also given equal access to development opportunities".
He said 17 State Minorities Commissions were in existence and more such commissions were being planned in other states.
Rehman Khan meanwhile said the constitution was being wrongly interpreted to deny minorities their legitimate rights by denying reservations.
Khan said a "new tendency is emerging to interpret the constitution in such a way to deny the legitimate rights of religious minorities as based on religion.
"When minorities demand reservation based on the backwardness or demand certain affirmative action from government to better their economic backwardness, it is turned down as no reservation or affirmative action could be taken based on religion."
Khan added such reservation would be in tune with the spirit of articles 15 and 16 of the constitution.
Article 15 talks about prohibition of discrimination on grounds of religion, race, caste, sex or place of birth and article 16 is about equality of opportunity in matters of public employment.
"The ministry is looking into recommendations of the Justice Ranganath Misra Commission for identification of socially and economically backward sections among religious and linguistic minorities and to recommend measures for welfare," Khan said.
The National Commission for Religious and Linguistic Minorities, headed by former chief justice Ranganath Misra, suggested that instead of the 27% reservation for Other Backward Classes (OBCs), 15% be set aside for Muslims and Christians, leaving 12% for the OBCs.
Khan said the issue could be addressed by treating each religious minority as a class of citizens and not as a religious group.
The UPA government had announced a 4.5% quota for backward minorities which was quashed by the Andhra Pradesh High Court, which said religion-based quota was constitutionally invalid. The government has moved the Supreme Court against the order.