Lamborn has been remanded in custody to reappear later this month.
Jack Lamborn, who heads up the church's senior pastoral role with wife Sari, said while his son was arrested on church grounds, the arrest was unrelated to the church's operations.
Jack said his son had been living in a cottage on the church property for about a year.
A police spokeswoman said police had searched in the area of Te Mata and Mangateretere Rd, Havelock North, under warrant about 8.50am on July 29.
"As it relates to an ongoing investigation we're unable to provide anything further at this time."
Jack said it was a "heartbreaking" situation.
"We have a daughter-in-law now who is on her own ... and a couple of grandchildren who are missing their dad."
The church offers on-site accommodation to people getting back on their feet, he said.
"We see it as a great opportunity for us as a church to be able to help somebody until they got their feet on the ground," Jack said.