Police said Krishnappa, who owns the building in Vidyaranyapura locality, and his accomplice Balaraj were arrested within hours of the incident.
"We have arrested Balaraj and Krishnappa for setting on fire a Christian prayer hall in early hours today," Deputy Commissioner of Police (North) T R Suresh told PTI here.
The duo was also charged with lodging a false case earlier against the neighbours -- Fayaz and Shardamma, who are at loggerheads with Krishnappa over a land dispute for the last 25 years.
However, during the investigations police found Krishnappa and Balaraj guilty of setting the prayer hall on fire, which was doused by themselves with the help of some people present there, Suresh said.
Krishnappa hatched this plan to take revenge on Shardamma and Fayaz, who had earlier lodged an attempt to murder case against Krishnappa.