Green Party co-leader Russel Norman is calling for Conservation Minister Nick Smith to resign, over allegations that the Nelson MP may have meddled in the submission process for a dam project in Hawke's Bay.

Dr Smith today denied this, and said he stood by what he told Parliament about the matter.

Dr Smith came under fire from the Greens in the House earlier this week, having to defend claims that he suppressed a submission document prepared by his department.

A draft submission by the Department of Conservation (DOC) expressed concerns about the risk of water pollution in the Tukituki River as a result of the Ruataniwha irrigation scheme, but only a shortened version was presented.

The Ruataniwha scheme is designed to be a long-term sustainable water supply solution for central Hawke's Bay. It has been deemed a project of national significance.

However, there are fears that it could have a negative impact on water quality in the region, where the water supply is over-allocated.

After revelations that DOC did not submit the full document, the Greens claimed this was because Dr Smith had effectively suppressed it.

The party said DOC submitted only two paragraphs - out of an intended 32 pages on the scheme - which did not mention concerns over water pollution.

In the House, Dr Smith denied interfering with the nature of DOC's submission, saying he would have been "negligent" had he not discussed statutory aspects of the Ruataniwha proposal with senior DOC staff.

But Dr Norman said today that a new email, which was reported by Radio New Zealand this morning, directly contradicted Dr Smith.

"[He] needs to explain why he said that he did not interfere with DOC's decision to pull its substantial submission on the planning regime for the Ruataniwha irrigation project, when it is clear that he did, and if he can't explain it adequately, then he needs to resign," Dr Norman said.

He said the deputy director-general of DOC sent an email to staff, stating that Dr Smith had concerns about the department's submission.

"This email demonstrates that Dr Smith did interfere in DOC's submission, but he denied that in Parliament on Tuesday."

Dr Smith said today that he "absolutely" stood by what he said in Parliament.

"At the beginning of July, junior DOC staff prepared a submission - a draft," he said. "I never saw that until Tuesday [this week]."

He said that at a regular weekly meeting with the department on July 29, he took part in a discussion on what the draft submission was about. Senior DOC officials told him that they believed it went beyond the department's brief, commenting on issues of water quality for which DOC was not responsible.

Dr Smith said that at that point, he asked to see the submission.

"I said, ‘Look, I've only got two sentences on this thing - I want to get a full brief, and I want to see the submission before it goes in'," he said today.

"Then I get a full brief on the Wednesday. It's about a 20-page document, and it sets out the department's decision as to why they're only going to submit on those narrower issues, and not the nutrient [water quality] issues."

Dr Smith said the brief included the revised submission, but the draft submission was not given to him with the briefing paper, and he did not see it until this week.

He said it was perfectly reasonable to request more information on an important issue.

Dr Smith said there was an internal debate going in within DOC, with senior staff concerned that they were over-reaching, and other staff wanting to make a submission on water quality.

DOC is responsible for the Tukituki estuary, into which water from the dam would flow.

Dr Smith said the issue of water quality would undoubtedly have some impact on the preservation of freshwater species, but DOC needed to pick its battles, and it had confidence that the National Institute for Water and Atmospheric research would provide a submission on water quality.