Lagos State commissioner for physical planning Olutoyin Ayinde also said that several other structures on the site of TB Joshua's Synagogue Church of All Nations (SCOAN) were sub-standard.
They included the vast main auditorium of the church, which Joshua describes on his website scoan.Org as an "architectural masterpiece" designed by the Holy Spirit.
"By our records, the collapsed building does not have approval," Ayinde told a coroner's inquest into the September 12 tragedy, which claimed the lives of 84 South Africans.
But engineers have indicated that the addition of extra floors without strengthening the foundations caused the collapse.
Ayinde said the main auditorium of the church, to which thousands flock every week to hear Joshua's sermons, had been given approval for five floors on January 1, 2004.
But subsequent inspections had determined that three extra floors were being added, in contravention of the approval, he said, calling the auditorium "structurally defective".
"The ongoing construction on the existing five floors to eight is not being professionally executed," he told the hearing.
State government inspectors also discovered a number of other unapproved structures on the sprawling church site and had stopped further development.
"By the additional construction we saw on site, we are inclined to express fears."
On the collapse of the guesthouse, Ayinde said he had reviewed security camera footage released by SCOAN officials which they claimed showed a low-flying aircraft above the building.