Transport for the North's business case for Northern Powerhouse Rail (NPR) was due to be handed in to the Department for Transport for consideration this month, with a decision due in 2019.
But it will not now be signed off for submission until February at the earliest after local leaders east of the Pennines raised concerns that the Manchester-to-Liverpool leg could be built before the trans-Pennine element.
The Yorkshire Post understands from multiple sources that leaders in West Yorkshire and Newcastle have both stressed to Transport for the North the importance of a 'whole network' approach rather than smaller elements being fast-tracked.
Last month, the Post revealed that Chancellor Philip Hammond and Transport Secretary Chris Grayling were considering whether the HS2 high-speed rail project connecting London to Leeds and Manchester could be extended to Liverpool.
It is understood any extension could form the first stage of NPR, but would happen more quickly than the rest of the scheme by using the statutory instruments already in place for HS2.
But the suggestion that the trans-Pennine element of the proposed route could be deemed less important has led to TfN being challenged by local leaders.
The lack of agreement meant the item last week at TfN's board where the strategic outline business case for NPR was due to be agreed was shelved at the last minute. It will go back before the board, made up of senior politicians from across the North, in February.
In a statement, TfN said a decision was taken "to make space for further fine-tuning, allowing members to feed-in fully and have chance to digest all the details."
A spokeswoman added: "This will not affect the overall timescale for the project and we are confident we will be ready for submission to Government early in the new year."
And TfN's Northern Powerhouse Rail Director Tim Wood said of the submission: "At this early stage – as is standard practice – a number of options are under consideration. And nothing is ruled out. This includes a variety of potential routes as well as options for how the network might be built."
"This is the first step of the journey, one where we prove Northern Powerhouse Rail is deliverable, affordable and transformational. There will be more detailed discussions to come as we move into the next stage of development."
He added: "We must grasp this opportunity, which will ultimately change the lives of millions of people and support thousands of businesses. The support for this programme remains as strong as ever and we’re still on track to deliver as planned."
The Â£35bn NPR scheme will shorten journeys from Leeds to Manchester, via Bradford, to half an hour and connect up to Sheffield, Hull and Newcastle. Transport officials say it is vital for delivering the 'Northern powerhouse' ambitions of creating a 'virtual city' across the North which would rival London.
Speaking to The Yorkshire Post at Leeds station this week, Rail Minister Andrew Jones said of the Northern Powerhouse Rail submission: "When Transport for the North are ready to publish it, I am ready to receive it. I look forward to receiving it.
"I am quite sure this proposal will benefit all parts of the North, it is from the North, for the North and backed by significant intent from the Government. We can't pre-judge where it is going to be because we haven't had the report yet.
"It wasn't really what was discussed at the meeting. The point I made about it is that Northern Powerhouse Rail is intending in its earlier discussions to use some of the HS2 infrastructure, so knowing what their plans are will influence HS2 planning, and we want to get on with HS2 as fast as possible.
"My point was, this is a great scheme for the North, we should be getting behind it. It is from the North, for the North, but don't delay."
Director of Northern Powerhouse Partnership Henri Murison said: “In the New Year, Transport for the North will be presenting a single compelling plan which will ensures Northern Powerhouse Rail delivers for the whole of the North through a comprehensive whole network approach.
“Building on the much-needed Trans Pennine Route and East Coast Route upgrade, the North will need to identify the most efficient mechanisms for the new Northern Powerhouse Rail infrastructure – including the Liverpool line from Manchester Airport, connecting to the HS2 tunnel into Manchester Piccadilly.
"The most sensible solution for this should be that HS2 be asked to build it. This could also be applied in other parts of the Northern Powerhouse Rail network and stations as well as Network Rail playing their part, for example delivering the HS2 connection to York as part of improving east-west connectivity in coming years.
“The Northern Powerhouse Partnership has never subscribed to the idea that the new line between Manchester and Leeds should open any later than when HS2 arrives in Leeds.
"The expertise which has been built up within HS2 on developing Hybrid Bills should be put at the disposal of all of the Northern Powerhouse Rail project, and that the sequencing of legislative time reflect fact that a new line through Bradford should open as early as possible to benefit people from Sunderland to Preston, including unlocking Manchester Airport as the international gateway to the Northern Powerhouse.”
In the most recent Budget the Chancellor pledged Â£37m to support the development of Northern Powerhouse rail, and a Department for Transport spokesman said the Government remained "fully supportive of plans for Northern Powerhouse Rail."
He said: "We look forward to receiving their proposals in the coming months. Decisions on next steps will be taken after we have received the business case. This will help ensure we take the right approach for Northern transport – so that all Northerners can benefit from our record investment."