The pledge two weeks ago was warmly welcomed by many as a sign that plans for the Northern Powerhouse Rail project connecting the great cities of the North had the support of government.
But behind the scenes, wrangling over the details of the scheme and how it will connect with the HS2 route between London and the North has caused tensions between transport officials and northern political leaders.
And the lack of agreement has led to fears that the arrival of high speed rail in the North could potentially be delayed beyond the long-promised date of 2033.
A major bone of contention is how Manchester's Piccadilly station should be extended to accommodate the 250mph HS2 trains from London and NPR trains to Liverpool, Leeds and the rest of the North.
Analysis by TfN, HS2 Ltd and Network Rail suggests a six platform, 400 metre station could be built above ground - extending the proposed HS2 station at the site by two platforms - for an extra £570m compared to the original HS2-only scheme.
But officials in Greater Manchester, led by Labour metro mayor Andy Burnham, refuse to back this and have argued strongly for an underground station to accommodate Northern Powerhouse Rail.
According to a confidential TfN document seen by The Yorkshire Post, costings by transport officials suggest such a station would need four 400-metre platforms and would cost £6bn. But Mr Burnham's team have cast doubt on the evidence used for the decision and say more work is needed.
The tensions are understood to have bubbled to the surface during the most recent meeting of Transport for the North's board, held in Leeds on July 31.
During the public section of the meeting the Greater Manchester mayor welcomed Mr Johnson's announcement and said northern leaders should not lower their ambitions.
He said: "Some of the things we are about to discuss at this meeting are the only time we will be ever do these things, and they will set conditions for growth in the North for the rest of this century."
And after the press and public were asked to leave, tensions rose as Mr Burnham challenged the plan to allow HS2 to go ahead with their plans based on a surface station and not his preferred underground option. A source told The Yorkshire Post: "It got a bit heated."
Time is ticking away on the project, with the Hybrid Bill for Phase 2b of HS2 due to be deposited next June as part of a timescale that would see the high speed route arrive in Yorkshire by 2033.
Any changes to the design - which currently includes a surface station at Piccadilly - would require further legislation, which the TfN document warns would need to get underway this summer to fit the current timescale. The next meeting of the authority's board is not until September 12.
One northern leader told this newspaper they feared the dispute might delay the arrival of NPR in the North or even put the whole project at risk.
They said: "If you are going to government and saying we want Northern Powerhouse Rail and there is unnecessary spending, that would provide a massive excuse not to approve it."
A Treasury source told The Yorkshire Post: "We have got a relatively sympathetic PM in Government but you need to be practical and realistic. If people are making excessive demands that are not universally supported, that is not going to be helpful. There is a finite amount of money, that is life."
In a statement, TfN said its work was not holding up HS2 from progressing its plans. A spokeswoman said: “It was agreed last week by our Board to come back in September following additional work on the various network options. This work is not holding up HS2 from progressing their current plans.
“We submitted a high-level business case to the Government in February for Northern Powerhouse Rail, which included several different options. We’re now working through these in more detail with both our members and the Department for Transport as our co-client.
"However, our northern leaders are clear that we fully expect a commitment from Government to the £39 billion network to connect all of the North’s cities with a fast and reliable railway.”
Henri Murison, Director of the Northern Powerhouse Partnership, which represents civic and business leaders, said: “The speech made by the Prime Minister last month made clear the need to accelerate progress on Northern Powerhouse Rail – which must be the focus of all those of us involved in the coming months.
"We must ensure the project reflects the settled will of the North’s leaders - including a Bradford City Centre station. The Prime Minister has made clear that the will of the North must be the basis for the scheme he wants to see in the autumn agreed.
“Further work on underground station in Manchester is not delaying HS2 or Northern Powerhouse Rail – and is the right thing to do because there is significant further work being undertaken to find a solution which works for the North, and isn’t one designed and dictated to us by officials from Whitehall."
Junction south of Leeds would be too disruptive, says TfN
Leaders in West Yorkshire could also be disappointed as the current plan for the design of HS2 does not include a 'touchpoint' in Stourton, south of Leeds.
This measure would have allowed HS2 and NPR services approaching from the south to loop round and pass through Leeds station - which is designed with trains coming in from the east and west - rather than terminating in the city or passing through altogether on the way north.
But in its report, written by its NPR director Tim Wood, TfN says creating this junction would lead to "significant disruption in south Leeds and significant impacts upon local employment sites", with a £800m cost much higher than originally thought.
Officials now say alternative options are available using the proposed HS2 station at Leeds, which would be built south of the existing station, combined with infrastructure work in South Yorkshire which would cost less and "avoid the complex delivery issues at Stourton".
A spokesman for West Yorkshire Combined Authority, which makes transport decisions for the county, said the benefits of a touchpoint "include the possibility of new routings between the North’s core cities with greater opportunities to release additional capacity and reshape the national network".
He said: “We also want to see HS2 services to reach wider markets beyond Leeds, such as Bradford, Huddersfield and, further afield, Hull, which could mean high-speed services arriving in Bradford 10 years ahead of the completion of Northern Powerhouse Rail.
"The benefits could also boost the commercial benefits of HS2’s eastern leg and also provide the potential for new markets such as the North East and the East Midlands as well as supporting more efficient operations through enhanced connectivity.”
Henri Murison of the Northern Powerhouse Partnership said: "The point of the Stourton junction proposal is to enable trains from the new HS2 line to carry on to Bradford, enabling better connectivity to cities like Sheffield, and ensure the system has resilience.
"Many focused on the case for NPR are open to all ways to achieve the same benefits – but until we see the detail of any alternatives no one should rule it out from further consideration.”
An HS2 Ltd spokeswoman said: “We continue to work on the detailed design of Phase 2b route between Birmingham and Leeds, and Crewe and Manchester, in line with the projected timescales for the hybrid Bill submission.
"We revised our hybrid Bill submission date to enable more time to work with Transport for the North and explore all potential opportunities to align HS2 and NPR, as we’re determined the North gets the best possible transport system.
"HS2 is essential to Transport for the North’s plans. Together, we will enable faster, more frequent and reliable rail services, making it easier for people and businesses to live, work and trade where they want.
"HS2 will give passengers thousands of extra seats every day, and will move intercity trains off the busy existing rail network, freeing up space to run future NPR services.”