Modi ordered a police crackdown after a Catholic school was burgled overnight in the Indian capital, forcing its closure for the day, the sixth attack on a Christian building in the city since December.
"Prime Minister Modi called me over the recent cases of vandalism of Delhi churches and strictly instructed (us) to track down the culprits," commissioner B S Bassi told reporters.
"We have increased security around churches and are taking the case with utter seriousness. He asked us to ensure no such attacks take place in future," he said.
Modi said in a statement he asked the commissioner to "speedily investigate the recent incidents of vandalism" but did not specify those on churches and the school.
Priests, nuns and parishioners clashed with police earlier this month as they staged a protest in Delhi over what they said were five church vandalism and arson attacks since December.
Clergy accused Modi's government of failing to speak out against the attacks which they blamed on Hindu hardliners.
Critics say hardliners have felt emboldened since Modi's Hindu nationalist Bharatiya Janata Party (BJP) stormed to power in general elections last May.
Police said burglars broke six CCTV cameras and stole about 8,000 Indian rupees ($128) from donation boxes at the Holy Child Auxilium School, but said the attack did not appear to be motivated by religion.
Father Dominic Emmanuel, spokesperson of the Delhi Archdiocese, rubbished the comments, saying there was a clear pattern of attacks against Christian institutions.
"Police are trying to take an escape route. No one will break into a school with an intent to steal money, it wasn't a bank," Emmanuel told AFP.
"The police are not taking matters seriously and are downplaying the incidents by terming them petty crimes," he said.
Police denied dragging their feet on the other cases, including one this month in which church ceremonial items were stolen and an arson attack on a church in December.
"We suspect it to be an insider's job as they knew exactly where cash was kept," Bassi said of the school break in, adding, "the cases of vandalism will be solved soon."
Hardliners have been accused in recent months of trying to convince Muslims and Christians to convert to Hinduism, sparking outrage from political opponents in parliament.
While Hindus account for more than 80% of India's 1.2 billion population, the country is officially secular and is home to sizeable numbers of Muslims, Buddhists and Christians.
Christian school vandalised in South Delhi
A Christian school in Vasant Vihar area of south Delhi was vandalised by a group of men in the early hours of Friday morning, The Times of India reported.
The police identified the school as Holy Child Auxilium which was shut down after the attack and the children were sent home for the day. This is the sixth such attack on a Christian institution in the last 12 months.
The identity of the perpetrators has not yet been disclosed by police but footage revealed that they were three to four in number and were wearing masks.
Police confirmed that the principal's office was vandalised and Rs8,000 cash was missing.
Senior police officers, forensic officials and crime teams arrived at the scene and will be collecting evidence.
An FIR has been registered at Vasant Vihar police station and investigation in underway.
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