Transport for the North (TfN) has argued that a "phased 20-year pipeline of rail investment" is needed to help the northern economy after the pandemic and unlock its future potential.
The strategic transport authority, whose board includes metro mayors and business leaders, made the case in its submission to the Government's Integrated Rail Plan.
It was announced earlier this year by Boris Johnson as he revealed that HS2 would go ahead despite opposition from Tory MPs and would be treated as part of an "integrated masterplan" named High Speed North.
In its submission to the National Infrastructure Commission, TfN makes the case for major projects to be carried out in a "phased" approach that would allow some elements to be finished earlier than currently planned.
But it said local and regional improvements to the existing congested rail network are needed to unlock freight and passenger capacity in the shorter term.
Prior to the start of the pandemic, when passenger numbers dropped to near zero, performance of the North's two main rail operators was so bad that one was taken into public hands. Congestion and a lack of capacity on the network are seen as two of the major factors behind their struggles.
TfN's submission said: "Whilst we understand the focus on capacity and connectivity for this inquiry, the North’s rail network is already constrained by reliability and lacks resilience.
"There are a number of locations that lead to reliability issues which can spread across the North.
"These are in major city locations and on key national routes. Investment is needed in the current rail network to address these issues and to allow the North’s existing network to achieve the agreed minimum standards."
It calls for "quick wins" on the existing network, with an immediate focus on Manchester and Leeds hubs, and for outstanding work to tackle bottlenecks to be completed.
TfN chief executive Barry White said: “We’ve strongly welcomed the Government’s passion for infrastructure investment in the North, and commitment to projects like HS2 and Northern Powerhouse Rail. It’s an agenda the North set.
"But there’s no point in doing it piecemeal. Now, more than ever, the North needs certainty on what rail schemes will happen and when, so that passengers and businesses can benefit as soon as possible.
“We need an integrated and sustained 20-year pipeline of investment in our rail network. It’ll be a vital weapon to combat the COVID-19 economic shock and to secure a greener future. Better rail infrastructure could get people and the economy moving and, in the long-term, support a period of growth that creates more opportunities.
“We’ve been clear that tackling rail problems in the here and now – by committing to projects around some of the congested parts of the North’s network – need to be considered by the Government and then progressed at pace.
"But we also need to explore how to speed up delivery of key parts of HS2 and Northern Powerhouse Rail in the North to ensure people aren’t waiting decades for change. We must deliver on the well-worn promise that change is coming down the track.
“Our Members are clear on what interventions are needed, and that – as a formidable joint voice for the North – they should have a strong role in the decisions and the delivery of such rail schemes.
"The North is speaking with one voice through this evidence-based submission, and we stand ready to work together with Government through the next steps.”
In the terms of reference for the Integrated Rail Plan, the Government says that based on current plans, Phase 2b of HS2 connecting Leeds and Manchester with the Midlands will "deliver connectivity for the East Midlands and the North considerably later than the rest of HS2".
It adds: "The Government wants to ensure that Phase 2b of HS2 and other planned rail investments in the Midlands and the North are scoped and delivered in an integrated way, including with the wider rail network, whilst driving down unnecessary costs and over-specification."
In his speech to the Commons in February, Boris Johnson said: "Those who say we should simply build 2B and Northern Powerhouse Rail according to the plans currently on the table, are effectively condemning the North to get nothing for 20 years. And that would be intolerable.
"So as we draw up this plan we are not asking whether phase 2B is not to be. That is not the question, Mr Speaker The question is how we can bring a transport revolution to the North sooner."
Amid fears the Leeds leg of HS2 may be delivered after the Manchester leg, Leeds City Council leader Judith Blake the Government "must commit to delivering Northern Powerhouse Rail alongside the eastern leg of HS2 and the full TransPennine Route Upgrade, so the North can benefit from increased capacity and connectivity, and to support our economic recovery from the COVID-19 pandemic".
But Tees Valley metro mayor Ben Houchen said TfN's sumission emphasised that "investment for crucial local and regional improvements should not be overlooked".
He said: "There is a need for a rail network that truly serves the whole of the North, and isn’t just focused on the big cities."
A Department for Transport spokeswoman said: “We welcome all submissions provided to the National Infrastructure Commission during its call for evidence on the Integrated Rail Plan.
“Our absolute focus is delivering the transport infrastructure that communities in the North and Midlands need to maximise future opportunities and prosperity.
“The Integrated Rail Plan will be published by the end of the year.”