"In all my dealings with Mr Feeley as the chief executive of the council and his previous public servant roles, I have found him to be a person of total integrity, and I have not seen anything that would give me cause for concern.
"But it's proper the auditor-general is able to do that investigation without a minister pre-judging in any way that inquiry."
The Rafa Trust lodged an application for a 20-section subdivision on the southern edge of Arrowtown last December.
The auditor-general's office announced its inquiry on May 29 at the request of members of the public. It is examining Feeley's involvement in developing the council's housing accord and special housing area policy.
Dr Smith would not be drawn on whether the council had erred in not setting aside the Rafa Trust's application while the inquiry was under way.
It was up to the council to decide which applications it considered for recommendation to him.