The blaze broke out around 1 a.m. at St. Cyril and Methodius church on Jacques Street.
Flames destroyed the roof of the parish.
"The roof went very quickly, it went from the back of the church toward the front of the church," said Perth Amboy Fire Chief Ben Ruiz. "We started to evacuate, went to the rectory and notified the pastor, who was asleep and had no idea."
Two homes behind the church also had to be evacuated. There were no injuries.
The pastor said he believes the 90-year old church can be rebuilt, despite suffering extensive damage. It is part of the Polish National Catholic Church.
Word of the fire spread quickly through the city's Peruvian community that their church, which honors a miracle of a church in Lima surviving an earthquake centuries ago, was burning down.
"I couldn't believe it because we worked hard at this church to make it better, to make it pretty," said church member Cynthia Sanchez.
Investigators are trying to determine the cause of the fire.
For more information on how you can help, call 732-510-9552.