He said an impartial inquiry has been ordered into the recent incidents as a delegation of Christian leaders met him to say that five churches were attacked in the last two and a half months in Delhi and holy relics and holy communion were destroyed but police was doing nothing.
The home minister told the delegation that the government would not tolerate any discrimination on the basis of caste, colour or religion, a Home Ministry official said.
Singh also instructed Delhi Police Commissioner B S Bassi to make proper arrangements for the security of churches and other places of worship, he said.
The delegation gave a memorandum to him demanding security for Christians and their places of worship.
Meanwhile, members of the community staged a major protest in the city on the eve of assembly polls, accusing the government of inaction and wondered why Prime Minister Narendra Modi was silent on the issue.
Police detained over 200 protesters from outside the Sacred Heart Cathedral in central Delhi when they tried to march towards the residence of the Home Minister in a high security area.
A number of priest and elderly persons including women were picked up police and forced into buses. Some protesters, carrying placards, squatted on the road demanding protection to the churches.
Father Dominic Emanuel, a senior leader of Delhi Catholic Archdiocese and a number of elderly persons were seen picked up police and forced into buses. Some protesters, carrying placards, sought justice to the community and protection to the churches.
"We have detained the protesters and they have been taken to Parliament Street police station. They did not have permission to protest outside the church and we cannot allow them to protest on public roads," Joint Commissioner of Police Mukesh Meena told reporters.
Some protesters were critical of the prime minister saying though he was speaking extensively on different issues, he did not utter a single word on the "attacks" on churches.
"Why the prime minister is silent on the issue. We are very sorry and sad," said an elderly protester.
Father Savarimathu Sankar, spokesperson for the Delhi Catholic Archdiocese, wondered why the administration has been "ineffective" and was not taking action against those allegedly involved in such "attacks".
"The prime minister claims to be a very strong PM. What happens when it comes to ground realities? When you are not being able to protect a small minuscule community how are you going to protect the whole of India. This is happening right in Delhi," he said.
In the fifth such incident since November, a church was allegedly vandalised by some unidentified persons earlier this week in South Delhi's Vasant Kunj area, sparking outrage among the Christian community which alleged that it is part of a "hate campaign".
"We have given representations to the president and the prime minister but there has been no follow up from their side. This is the fifth incident and it is apparent that the incidents were of communal nature," he said.
After the meeting with Rajnath Singh, Christian leader John Dayal said, "Police has done nothing and they have described the incidents as simple theft, burglary and trespassing. We told the home minister that these were not simple incidents but attack on our religious places."
Following their demand, Singh has directed the police to insert certain provisions of the Indian Penal Code like "provocation with intent to cause riot, hurting religious sentiment" etc in the FIR, in cases of alleged discretion of churches, he said.
Francis said incidents of alleged attacks on churches have increased in the last six months and demanded setting up of a special investigating team for probing the five incidents of alleged violence against churches. He said the probe should be monitored by the Delhi high court.