The woman in her 70s was left critically ill on Saturday after being attacked by thieves at her school and convent in West Bengal.
Narendra Modi said he is "deeply concerned" by what appears to be a targeted religiously motivated attack.
The rape followed a number of other recent attacks on churches across the country.
In Haryana province a Catholic church had its cross removed and replaced with a statue of a Hindu god.
Dr Sam Paul from the country's National Christian Council told Premier the Prime Minister's intervention didn't mean much.
He said: "They are not talking enough action in Delhi.
"They just said it was a small incident, even the Prime Minister when he made this statement said don't make a big issue out of the small things.
"He said it because of international pressure, it didn't come heartedly.
"We want his saying to be action."
Mass protests have been taking place across India with hundreds of Christians and Hindus taking to the streets to urge better protection for religious minorities.
Premier's Antony Bushfield speaking to Dr Sam Paul: