Dr Smith has denied having influence over the changes to the submission and says he was unaware of the draft version until last week.
A leaked email last week showed Dr Smith was briefed on the fact DOC was preparing a submission and that he expressed concern about it. He says those concerns were about the brevity of the information he'd received during that briefing which amounted to just two sentences.
Mr Sanson said he stood by the decision taken by his senior managers not to submit on the wider environmental aspects of the proposal and said Dr Smith did not direct DOC about the submission it was making.
However Mr Sanson said he did have questions about the time frames for making final decisions on the submission.
He had also initiated an internal investigation into the unauthorised release of a departmental email in connection with the submission.
"The release of these emails calls the department's integrity into question" and he had asked an independent reviewer to look into this issue.
A DOC spokesman confirmed a staff member involved in the preparation of DOC's submission recently resigned, but would give no further detail.
Mr Sanson also said he would not comment further on either of the enquiries while they are underway.
This morning, Dr Smith continued to deny any knowledge of the draft submission until last week.
"To say that because you got two sentences that you know what's in a 34 page report is a very big stretch."
"I think you are dancing on the head of a pin to say that I knew about a 34 page submission because I was told a submission was being prepared."
But Labour Leader David Cunliffe said it was Dr Smith who was "he's dancing on the head of a pin" about what he knew and when.
While there was "a lot of murk" around the issue, the fact was "suddenly after Nick Smith's meeting with his officials a 34 page document turned into two paragraphs".
"There's a lot more to come out about this story."
Asked whether he believed Dr Smith had a hand in the report being altered, ``I'd say he's had his arm in it" Mr Cunliffe said.