But CEO Nic Blakeley said if issues were substantiated, employment action would follow.
An independent report has identified major flaws in MBIE's handling of a biometrics upgrade project, which wasted more than $30m.
The Public Service Commission will investigate officials' behaviour.
Minister Erica Stanford claims she was misled by officials who avoided Cabinet scrutiny.
Analysis - National MP Grant McCallum spoke for the room, repeatedly muttering "Jesus!" as Erica Stanford levelled extraordinary allegations against her own ministry.
Immigration Minister Erica Stanford says she was 'furious' she was misled.