The attack on Convoy Presbyterian Church has been described as an assault on the entire Christian church by its minister.
Rev Colin McKibben of Convoy Presbyterian Church, near Raphoe, said the incident took place between 4am and 5am on Friday.
The fire the Presbyterian church and nearby Orange hall in Co Donegal are probably the work of the same people, the minister added.
“The people who probably did that came up to the church, knocked in the door of the minister’s room at the back and set fire to a large pulpit Bible,” he said.
“Then they moved into the main church and set a fire to papers at the pulpit, pulled down and smashed two standard lights and started a fire in the floor of the pulpit.
“The entire community is hurt and shocked.
“This is not an attack on a Presbyterian Church, this is an attack on the Christian church at large.”
The community works very well together “with great affection” on many cross community projects, he said.
Local Catholic priest Fr Philip Remmy said he was “saddened” because it was “a desecration of what people hold very dear”.
The Moderator of the Presbyterian Church, Dr Michael Barry, said: “I have been appalled to hear of this attack at our Convoy Congregation.
“It is very upsetting for our fellow Presbyterians to have their place of worship broken into and an attempt made to destroy it.
“There is a small Presbyterian community in Convoy who work alongside others in the community and from what I hear, relationships are good, so this news is disappointing to hear especially when all the community work so well together.
“As I have said in the summer, places of worship should not be the target of any attack.
“I condemn this religious hate crime on one of our Churches and ask those involved to have more respect for their neighbours.”
Gardai said they are investigating criminal damage.
It is hoped the church will be open for worship on Sunday.