Waikato Regional Council included commuter rail in it's long term plan but there's no guarantee it will go ahead.

A commuter train between Hamilton and Auckland could leave the station by the end of the year as the Government treats it as a priority.

But there are obstacles in the way of the interim rail service between the cities.

Without a 75 per cent funding commitment from central government for the twice-daily interim service, Hamilton City Council, which have taken up the project after a decade of public advocacy, will pull out.

Waikato District Council support a business case being developed but can't help with funding; Auckland Council supports commuter rail but not the interim solution in its current form, while the New Zealand Transport Agency can not support rail proposals under its current policy regime.

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The Government is having to rejig policy and in a letter, received Wednesday, from Minister of Transport Phil Twyford, he intends to progress work on the Hamilton to Auckland service "as a matter of priority".

"In addition to this rail service, I am keen to work more closely with you and other key stakeholders in the Waikato region, to advance development of the Auckland-Hamilton corridor as part of a wider regional growth initiative," Twyford said.

The Labour-led Government prioritises rail for public transport and freight but a revised Government Policy Statement is still in the works. No timeframe has been set for a decision, he said.

In lieu of a decision from Wellington, Hamilton City Mayor Andrew King and councillor Dave Macpherson led a delegation to the Waikato Regional Council chambers on Wednesday asking for the interim rail solution to be included in its 2018 to 2028 Long Term Plan.

"What we're asking for, is for you to vote this through and keep this option open," King said. "Vote this through, keep it in the system, put it out for consultation and by then, central government will have their intentions known."

Hamilton's city infrastructure general manager Chris Allen said the service could be up and running within 18 months, all going well.

"We think it could be the 2018/2019 year . . . which could put you into the end of the calendar year, this year."

The proposed budget would see the New Zealand Transport Agency fund a $6.5 million share with the regional council footing a $2.1m share with an estimated 97,000 passengers paying $10 per one-way fare.

Hamilton ratepayers will also foot a $30 impact on their rates bill - based on the median property value - to fund the service. Of that, $25 will go towards operational costs and $5 to the cost of the rail cars and engines.

That comes on top of a city council rates hike they are already facing and a regional council proposal to lift its general rate by 6 per cent

The majority of councillors accepted the rail proposal but Cr Jane Hennebry​ voting against.

She said there is a lack of clarity around the rates impact on all properties in the city and there is potential for it to go ahead even if Government funding dips below the 75 per cent target.

"It needs to be really clear if you don't get the 75 per cent. You say you won't do it but it's only a little bit more if you get 60 per cent," Hennebry said. "I am not going to ask ratepayers to support this."

Cr Russ Rimmington said the decision is a "stellar" one.

"We need to make good courageous decisions as Auckland grows closer to Hamilton.

"This must proceed. We have a very strong letter supporting it. We might not get over the line, it might be a 50 per cent chance but let's give a a chance."

Cr Dal Minogue replied to Rimmington: "What Donald Trump is to international relations, Russ Rimmington could be to rates increases," Minogue said. "I'm skeptical about where things are going at the moment."

Cr Hugh Vercoe said there is no risk to council in including it in the long term plan.

"If Hamilton City came here saying they had the 75 per cent subsidy, I believe it wouldn't be a discussion," Vercoe said.

"While they haven't got confirmation yet, they are saying: 'Put it in the plan, come time to adopt the LTP if the government have not stumped up, Hamilton City will pull it out."

Cr Bob Simcock was nervous about not having enough information for the community to digest.

"My nervousness is that if we get push back because we don't have a clear enough proposal by the time this goes out, then the project dies for six years," Simcock said. "The less clear it is, the easier it is to destroy."