Scott said fire crews were on the scene pretty smart and got to work on the church, spraying it with water in an attempt to extinguish the large blaze.
Ean Dawson had been at his sister-in-law's house for around 30 minutes when he first noticed smoke rising before capturing dramatic footage of the blaze.
"We were just watching it from the deck … when I first noticed there was smoke I thought it was coming from a chimney," he said.
"About five minutes later I saw it coming out of the church and realised it was a fire and started recording."
Other witnesses described how clouds of black smoke were billowing into the sky, with one saying "the flames are absolutely huge, I'd say it's getting other properties".
A Herald reporter at the scene said the church building was completely destroyed.
"The church is black. The whole sky was all brown and black when we showed up.''
Photos of the blaze show flames leaping from the building and clouds of black smoke snaking into the air.
A fire service crew member could be seen on a cherry picker, with water being sprayed over the blaze.
"It stinks like smoke and there's a burnt, horrible smell in the air."
About 100 members of the public looked on as firefighters fought the blaze.
Just after 5pm, it appeared firefighters were heading into the building.
Witnesses said the building was the church hall but was not used by the church because Auckland Council deemed it unsafe. They said squatters lived in the hall.
The witnesses were in church this morning before going away for lunch, however, they spotted the flames and decided to investigate, thinking it was a house fire.
Upon arrival the witnesses said they were "surprised and shocked".
A man who lives about a block away told the Herald he was at home early this evening when he noticed cars stopping on the road.
He looked out to see smoke and flames jumping out of the church building.
"It happened so quick,'' he said.
Firefighters remained at the scene at 5.30pm, and were still working to secure the building.
In February the Herald reported that people had been warned to stay well back from the church's historic but "dangerous" Auckland Sunday school hall, whose repairs no one had been willing to finance.
Developer View West earlier wanted to build several apartments within the St James church precinct on the corner of View and Esplanade Rds. It also wanted to demolish the hall fronting Esplanade Rd and build more apartments there.
Both buildings have a B-grade heritage listing with the Auckland Council. Both are owned by the Presbyterian Church Property Trustee. The council assessed the property's capital value to be $6 million last year.