Fresh allegations have been raised in Parliament about whether another Government agency had its criticism of the proposed Ruataniwha dam, in Hawke's Bay, suppressed.

The Green Party told Parliament GNS Science lost a contract after raising serious concerns about the accuracy of groundwater modelling on the Tukituki River.

Last week Radio New Zealand News revealed the Department of Conservation (DoC) discarded a lengthy and highly critical draft submission on the dam in favour of a few lines.

In Parliament on Thursday afternoon, Greens co-leader, Russel Norman asked whether GNS Science had its contract terminated by the Hawke's Bay Regional Council because it thought the council's modelling on the dam was wrong.

"Did the minister know that GNS scientists raised serious concerns about the accuracy of the regional council's ground water model, the fundamental information underpinning the work," Dr Norman asked.

On behalf of Science and Innovation Minister Steven Joyce, Government minister Nikki Kaye confirmed one of GNS Science's four contracts with the council was not completed but did not say why.

Dr Norman asked whether the minister knew two scientists who had worked on that contract no longer worked for GNS Science.

Ms Kaye replied she did not but said there are many reasons for people changing jobs.

Ministry reveals concerns

The Ministry for Primary Industries has revealed it had concerns about the dam, despite not mentioning them in its submission to the Board of Inquiry considering the project.

A leaked DoC draft submission, which was not submitted, said the ministry shares concerns the dam project could make the Tukituki River toxic and may not be economic.

The Labour Party said the concerns were considerably watered down in the ministry's final submission and it did a U-turn on the economic impacts. The party said it raised questions of political interference.

The ministry, which co-funded the dam's feasibility study, issued a statement saying the water project proposal provides an opportunity for economic, environmental and social benefits.

However, it also said it was seeking clarity around water management issues.

The ministry said while it had concerns about water quality, its minister did not tell it what to submit.

Just two government ministries - the Ministry for Primary Industries and DoC - made submissions on the water storage project, despite ministers classifying it as a project of national significance.

The Ministry for the Environment did not submit, even though Conservation Minister Nick Smith said it had a responsibility for water quality in the country's rivers.

The Treasury did not submit any economic analysis and Te Puni Kokiri did not offer a submission, despite widespread Maori concerns about the dam project.