"It's a huge financial contribution the Government is providing [for the roading infrastructure] and we have to keep our focus on that first and foremost."
The expressway is expected to be completed in about 2018.
Waikato Mayor Allan Sanson said the expressway was also his council's main priority.
"The commuter rail is nice to have provided we can afford it and it ticks all the boxes on the way through, but there's a few boxes it's not ticking."
No access to Britomart was one issue and the other was the length of time the trip was expected to take.
"It's around about two hours 20, it's just too long. Those two things alone make it very difficult for us to sell it to the community."
The idea is that the 96-seater Silver Fern railcar would leave Hamilton's Frankton Station at 6am, stopping at a station to be built at The Base, as well as in Huntly, Te Kauwhata, Tuakau, Papatoetoe, The Strand in Parnell and arriving in Newmarket at 8.27am.
An off-peak service would leave Auckland at 9.30am, arriving in Hamilton at 11.45am, leave again at 2.30pm and arrive at The Strand at 4.45pm. The final trip would leave Auckland at 5.30pm and arrive in Hamilton at 7.45pm.
It is estimated the service could carry up to 130 passengers a day with fares costing about $24 one way.
Mr Sanson said a proposal to run a train from Tuakau to Pukekohe to a park-and-ride service there was "less challenging and more beneficial" for the Waikato District Council.
A multi-agency working party has been investigating the trial for two years.
The Hamilton to Auckland rail working party's final recommendations to Hamilton city, Waikato regional and Waipa and Waikato district councils are that they agree to the two-year trial and invite public submissions.
The regional council transport committee chairman and chairman of the working party, Norm Barker, said: "Times are really tough at the moment and people are finding it really difficult to meet their obligations".
Hamilton City Council finance and monitoring committee chairman Dave Macpherson agreed no access to Britomart and the time the trip took were issues but they weren't "show-stoppers".