The NAB investigation team also questioned two officials of SBCA.
The NAB officials questioned Director Legal and Director Admin of the authority, sources said.
The team also scrutinized the SBCA record of the buildings constructed during last few years.
The sources said that the raid was conducted over the information received from deputy director town planning Nadeem Khan.
More arrests can be made from the building control authority in coming days, sources added.
A team had raided the SBCA offices on Tuesday and arrested deputy director Nadeem Khan and confiscated the record. The official was allegedly misusing his powers and facilitating the land grabbers for illegal encroachment of the government land.