Making a statement in the Assembly Fadnavis said the arrested persons have "confessed" to the crime.
They were identified by police as Rahul Patil (39), Anil Chavan, Laxman Sugvekar (21) and Mohmmed Tabrek Sheikh (19).
Fadnavis, who also holds Home portfolio, said Patil ran a gambling den in the area which police had raided on March 19 and he suspected the church authorities had complained against him, which might have prompted him to plan the March 21 attack.
They also demanded constitution of fact-finding panels at city, taluka and district levels to curb similar incidents.
Police had yesterday announced a reward of Rs 10,000 for any information on the wanted.
According to Khandeshwar Police, the attack was carried out by masked persons, riding pillion on a motorcycle at around 1.30 AM on Saturday. They hurled stones at the Saint George Catholic church located near a bridge in New Panvel, about 40km from Mumbai.
A case had been registered against the accused under IPC Sections 295 (injuring or defiling a place of worship with intent to insult the religion of any class) and 427 (mischief), police said.
The church, belonging to the Syro-Malabar hierarchy, was built in 2007 with a capacity to accommodate over 800 people for prayer.
