The fire service was called to the blaze on Kaponga St in Mamaku about 1.15am.
The single-storey building was "well involved in fire" when firefighters arrived at the scene.
Crews from around the region were called and between 24 and 30 firefighters attended.
A St John spokeswoman said a 52-year-old woman was taken to Rotorua Hospital as a precaution due to smoke inhalation.
Mr Smith said police knew who the woman was and she was not involved with the cause of the fire.
A spokeswoman for the Lakes District Health Board said the woman was treated and discharged.
Waiapu diocesan registrar Colleen Kaye said the church had been de-consecrated in 2012 and the local parish had not been using it.
"They have been looking at selling it," she said.
She said one of the stained glass windows had been removed and put into St Barnabas Church in Ngongotaha.
The window had originally been installed in 1951 at St Peter's to commemorate Mamaku families who lost sons and husbands in World War II.
Mamaku Anglican churchwarden Diana McArthur said the fire was "extremely upsetting" for the people of Mamaku.
"The residents had worshipped in there for well over half a century, we feel for them."
She said the property had been on the market, but they were now going to seek advice on what to do next.
A parish council meeting would be held tonight to discuss the next step, she said.
Mamaku resident Shane Hutchinson said the church had been there for years.
"It was a pretty church, I live a street over and everybody at the school was telling me so I thought I'd come and have a nosy."
Mr Hutchinson works at Mamaku School and said many there were feeling "very sad" about the fire.
Another Mamaku resident who did not want to be named said it was a "great shame".
"It was an old pretty church up on a hill... [I'm] feeling quite sad," he said.
Anyone with information should contact the Rotorua police on (07) 346 2968.
Information can also be given anonymously to Crimestoppers on 0800 555 111.