International Christian Concern (ICC) says so-called untouchable Christians and Muslims are not allowed support given to low-caste Hindus to progress in society.
The government has reportedly ruled they are not entitled to such scheduled caste benefits on the basis Christians and Muslims do not believe in the caste system.
ICC claims low caste individuals are treated the same whether they be Hindu, Christian, Muslim or Sikh and the Indian government's behaviour amounts to blatant discrimination.
More than 80-per-cent of India's 24 million Christians come from low caste communities and would be eligible for scheduled caste benefits if religion was not considered, the ICC says.
The ICC is quoting Pastor Solomon, the leader of a church in the Telangana State village of Todibiloli, as saying: This is an absolute injustice by the government.
"We go through [the] humiliation [of] the Hindu caste system as former untouchables as we [are] part of a Hindu dominant society. Caste oppression [exists], despite our religious affiliation."
Todibiloli is said to house a significant population of third-generation Christians from a low caste, locally known as "Mala".
Members of the Chrisian Mala community in Todibiloli have reportedly told ICC how they have can only collect water from the village well at a designated time, to avoid polluting high caste individuals.
Gaddapati Vijaya Raju, President of the All India Christian Federation, told ICC: "It is disheartening to see 66 years of [calls] for rights [by] Dalit Christians go unheard.
"This is in spite of recommendations by various commissions and political parties. We are simply asking the government to be fair and that the government delink religion from the scheduled caste benefits."
The Indian government says discrimination on the grounds of religion or caste is prohibited under the country's constitution.
A statement on the Indian government's website said: "The State shall not discriminate against any citizen on grounds only of religion, race, caste, sex, place of birth or any of them.
"No citizen shall, on grounds only of religion, race, caste, sex, place of birth or any of them, be subject to any disability, liability, restriction or condition with regard to (a) access to shops, public restaurants, hotels and places of public entertainment; or (b) the use of wells, tanks, bathing ghats, roads and places of public resort maintained wholly or partly out of State funds or dedicated to the use of general public."