After the landslide victory of the UPA government over communalism, the CBCI said it hoped the new government would "keep its promises of safeguarding the country from communal and divisive forces".
The Congress party and allies won 261 of the 543 seats in parliament, forcing the Hindu-nationalist Bharatiya Janata Party to concede defeat.
The Catholic body welcomed the decision of the majority to vote for a secular and progressive government.
"The apex body of the Catholic Church in India is pleased to know that the Indian voters have made a right choice in placing their faith in the UPA to lead the country for the next five years," it said.
Concerned over minorities in the country, the CBCI urged the UPA government , however, to "restore confidence among all sections of people particularly among the religious minorities for providing a stable, secular and democratic government".
Last August, Christians were violently attacked by Hindu extremists in the eastern state of Orissa after being blamed for the murder of a Hindu fundamentalist leader, despite Maoists taking responsibility. Attacks continued as Indian state governments were criticised for their failure to control the violence by Hindu radical groups.
"The Christian community in India has always supported political parties who have stood for the rights of the poor and the marginalised," the Catholic body stated.
Ebenezer Samuel, president of Serve India Ministries, said he was grateful for the election results and believed the outcome would "definitely benefit the growth of Christianity in the next five years", according to Mission Network News.
He was cautious in his praise, however, adding that he did not predict the persecution against Christians would come to a halt any time soon.
He told MNN: "Anything that happens can be blamed on the government, while they continue to perpetrate all kinds of cruelty against the minority."
