A late change of position by the Maori Party on a bill giving the Government power to replace Environment Canterbury's (ECan) councillors with commissioners was disappointing and unhelpful to the party's relationship with National, says Environment Minister Nick Smith.

The bill was passed under urgency on Wednesday night following a marathon debating session in Parliament, but the Maori Party, which had said it would support it, changed its position after hearing opposing arguments and consulting with South Island tribe Ngai Tahu.

Maori Party MP Te Ururoa Flavell said the agreement in its partnership with National meant it had to inform Dr Smith before voting in opposition - which it did - but doing so was its right.

He said the parties were not always in a agreement on issues and didn't believe the latest decision would cause too much of a rift between them.

"We have the right to disagree where we want to and go our own way, but it doesn't sort of bungle up into one huge splash where we all of a sudden throw our toys out of the cot and decide to go our separate ways," he told Radio New Zealand.

Dr Smith said he had kept the Maori Party in the loop over the proposed legislation and the late vote change was not helpful.

He said the party had initially publicly announced it would support the legislation.

"So it was a surprise that about half an hour before the third reading vote they advised us they had changed their position.

"I think it does put some pressure on inter-party relationships when you are dealing with difficult bills of this sort."

Dr Smith and Local Government Minister Rodney Hide announced on Tuesday they planned to get commissioners, led by Dame Margaret Bazley, in to replace ECan's councillors.

The move followed the release of a report which was scathing of how water management was being administered in the region.

It said there was no resource management policy and the community had lost faith in the councillors' ability to deliver on their statutory responsibilities.

However, there was a backlash following the ministers' decision from environmental groups and opposition MPs, some of whom suggested it would lead to consents being issued to corporate dairy outfits which were on side with National.

This week the majority of the Maori Party also voted against welfare reform legislation which aims to put more pressure on beneficiaries to return to work.