EMS rushed to the second-floor balcony of the Trinity United Methodist Church in White Plains around noon Thursday after a man cooking with a butane lighter caught fire.
Investigators said the victim, 53, whose name is not being released at this time, was known to them and they described him as occasionally homeless.
Witnesses said they saw smoke as first responders rushed to the scene at 130 South Lexington Ave. near the city's downtown.
"You couldn't see who it was or anything because they had a blanket over him," White Plains resident Jeff Jones said.
The Rev. Denise Pickett is the church's pastor.
She said the church offers weekly hot meals and operates a small food pantry. She added that neither was in service when the incident happened but believes someone who uses those services might have seen the church as a safe place to set themselves up.
"It's unfortunate that this situation happened and we will certainly pray for the family," she said.
The victim was taken to Westchester Medical Center, a Level 1 trauma center, in critical condition.
Police initially believed this was an accident but the investigation is ongoing.