Metro mayors Dan Jarvis Andy Burnham and Tracy Brabin say the imposition of a new timetable from next December to tackle the longstanding congestion issues in and around Manchester will mean the loss of a number of services.
Transport for the North has now written to the Department of Transport saying it will only accept this option if they get assurances about investment in northern rail services which help solve the problem long-term by increasing capacity.
South Yorkshire's metro mayor Mr Jarvis said it was "incredibly disappointing" that a Government Rail Minister had cancelled a planned meeting to discuss their concerns.
And the Labour mayor said leaders were being asked to agree to a timetable which would impact on the North's railways for years without having seen the Government's Integrated Rail Plan setting out its vision for major projects in the region.
If introduced the new timetable, dubbed the 'B+ option', would mean no services between Sheffield and Manchester Airport and that trains from York, Leeds and Huddersfield to the airport would be reduced from two per hour to just one.
The proposal came from the Manchester Recovery Taskforce made up of representatives from bodies such as the Department for Transport, Transport for the North, Network Rail and train operators.
If it was not accepted the current 'Covid timetable', which has much less capacity as it was designed for smaller numbers of passengers, would have to continue.
Transport For The North (TfN), the body responsible for coming up with a strategic transport vision for the region, has now written to the Government to say it cannot agree to the timetable unless certain conditions are met.
One is that the Integrated Rail Plan is published this month detailing what rail projects in the North such as HS2 and Northern Powerhouse Rail will be funded and when they will be delivered.
Another is that infrastructure schemes in Manchester enable TfN's long held commitment for new connections, including services from Bradford and the Calder Valley to Manchester Piccadilly and the airport.
They also want a firm commitment to reinstate the direct rail links between South Yorkshire and Manchester Airport if they are removed from next December.
In his letter to the Department for Tranport, TfN chief executive Tim Wood wrote: "The fundamental issue here is that the North is being asked to cut back its rall services at the exact moment the country is being asked to support economic recovery without any clear picture of when the required infrastructure to do this will be in place."
Dan Jarvis told a meeting of TfN's Rail North Committee that the process to reach this point has been "deeply unsatisfactory to say the least".
He said leaders wrote to the Government a few weeks ago and asked them to convene a meeting of the Northern Transport Acceleration Council so they could raise their concerns with a Rail Minister.
He told the meeting: "We were given the opportunity to do that and the Rail Minister committed to us that he would look at these issues and come back and discuss them further with us.
"It's therefore incredibly disappointing, I think, that as board members of the Rail North committee, we haven't had the opportunity to discuss our concerns more recently with Ministers.
"I also think that is not appropriate that we should be seeking to take very significant than long lasting decisions that will impact on rail connectivity across the North of England for years to come without the knowledge of what the Integrated Rail Plan will deliver for us all.
"So I think that the conditions that have been laid out, are really a precursor for certainly an agreement that I could offer to proceed down this road."
Greater Manchester metro mayor Andy Burnham said the North faced having a "substandard timetable" imposed with no date as to when it would be fixed.
He said northern leaders who had been "shouting into the abyss for years" about investment in services should accept the B+ option as the planning assumption so officials could get on with designing the services but reserve the option of being officially in dispute with the timetable change.
West Yorkshire mayor Tracy Brabin said leaders had been "pushed into a corner" and that if they were in the "last chance saloon" they might be forced to accept Option B+.
Northern rail services have been blighted for years by congestion due to too many services being squeezed onto railways that did not have the capacity to cope.
This culminated in the disastrous introduction of a new timetable in 2018 but despite action being taken services improved little in the months afterwards.
Experts trying to improve rail services as passengers return to train travel face the same problem as in 2019 that too many trains are travelling through the congested Castlefield corridor near Manchester.
The only solution is to take a step backwards and reduce the number of services to ease the congestion in the hope that extra investment in the coming months and years will increase capacity.
The taskforce came up with several options, all of which involved reducing the number of services in and around Manchester to ensure those that did run were more reliable.
According to TfN, these options were designed to improve performance in the short-term pending the delivery of enhanced infrastructure in the medium to long term.
After a public consultation a compromise 'B+' option was produced which rail officials say would deliver "significant passenger benefits".
Around 95 per cent of passengers would be unaffected by the recommended changes and passengers travelling to/through Manchester are estimated to save 100,000 minutes each day based on reduced delays.
But a number of services would be reduced or lost entirely, including trains to Manchester Airport from Sheffield and Newcastle and a reduction in frequency from Leeds, York and Huddersfield.
Mr Jarvis said: "At a point at which the Government are committing to level up the North of England, the loss of that connectivity, and the impact on our universities and our businesses across our city region would be very significant indeed."
At a meeting of Transport for the North's Rail North committee, rail consultant Richard George said there would be 'no winners but several losers' from the process and that he hoped infrastructure investment would mean hard choices could be avoided.
He said officials working on the December 2022 timetable needed some 55 weeks to plan the services so needed to start working on the B+ option now if that was what was to be introduced.
At the virtual meeting, Rail North committee chair Liam Robinson said discussing the issue of poor rail services felt like 'Groundhog day'.
The Liverpool councillor said: "This has been in the government's too difficult box for over a decade now and quite frankly it needs to be dealt with. I get quite frustrated that it feels that we're being given the bitter pill of B+ without being told the rest of the treatment package that we're going to get, get us back to full health."
He added: "I understand the Prime Minister is going to be making a speech tomorrow about levelling up, this is a classic levelling up issue. So it needs to be given the public attention it needs to actually get some movement on."
A DfT Spokesperson said: “We’ve been listening to people and have consulted widely on proposals to deliver improvements for rail passengers in Manchester and across the North West.
“We look forward to working with Northern leaders on both the current proposals to relieve the traffic jam of trains through the centre of Manchester, and on a longer-term plan for services and infrastructure.”