Conservative Ben Houchen, representing the Tees Valley, challenged his fellow northern leaders by claiming millions of people across the North will feel the two high speed rail projects would not benefit them.
During a meeting of Transport for the North he criticised what he described as an "over-concentration from local leaders and politicians and the media on Manchester and Leeds", adding: "We've got to look further afield from that."
Last month Prime Minister Boris Johnson promised to deliver the Leeds-Manchester leg of Northern Powerhouse Rail, a £39bn project seen as vital to improving east-west links in the North.
But there have been disagreements over how it will connect with the HS2 line connecting London, Leeds and Manchester, which is currently under government review and if built will arrive in Yorkshire up to seven years later than originally thought.
At a TfN meeting in Leeds in July, Mr Houchen and Greater Manchester metro mayor Andy Burnham clashed over whether a £6bn underground station - rather than an above-ground station costing a fraction of the price - should be built at Manchester Piccadilly station.
Mr Houchen told the most recent meeting of northern leaders at Manchester Airport that his comments were "certainly not meant as an attack on Manchester and Andy and the work that he does in his role as mayor". He added: "If I was in his position I would do exactly the same thing."
During a debate on what approach TfN should take to the two projects, the Tees Valley mayor said analysis done by his office showed the North East "has little to no benefit from HS2 or Northern Powerhouse Rail".
He added: "If you look at the current case for HS2 and NPR, it doesn't benefit the North East, actually large parts of rural North and East Yorkshire don't benefit in any way, shape or form, North Lincolnshire don't benefit very well at all.
"I welcome this discussion because it is about the fundamental principles of while we pat ourselves on the back and talk about how well we've done, at the moment we are missing entire swathes of many millions of people across the North of England who don't feel they are on the journey we are on with Northern Powerhouse Rail and actually practically are not on that journey.
"Even if we get to a point in 30 years time when the bloody thing is built, they are going to turn around and say 'well that didn't help us'. I do think that is something we need to address as an organisation about being a truly northern panel. At the moment, I don't think that we are."
TfN chief executive Barry White responded that the strategic outline business case for NPR "has a very significant investment in the East Coast Main Line, which does bring significant benefits to increase both the frequency and speed of trains to the North East."
He said: "So there is substantial benefit to Northern Powerhouse Rail. From the HS2 perspective, being able to get as far as York on HS2 and then getting on that improved East Coast Main Line will bring faster services to and from the South. That connectivity will be welcome."
But Mr Houchen responded: "I would have to dispute what you say about the North East on the basis that in theory NPR can benefit the North East of England through increased capacity and potentially high speed rail but at the moment Northern Powerhouse Rail doesn't include, for example, any improvements to Darlington station, which means you limit and cannot increase capacity and cannot run a high speed train into Darlington.
"Darlington is basically the gateway into the North East and therefore NPR and HS2 don't have, I believe, any material benefit or very little material benefit.
"That is something we need to capture and I know [TfN chairman John Cridland] has been lobbied very by me on the opportunity the Prime Minister has given us on the Manchester to Leeds line element of NPR.
"Actually to achieve some of the benefits of that you do have to improve what is happening in the North East and at the moment that is not being captured.
"Now we can capture it, but I just want to bring to the attention of this board that we are at risk of potentially not doing so and limiting not just benefits to the North East but also capacity between Manchester and Leeds by not doing those peripheral benefits in the North East of England."
TfN chairman John Cridland said his comments required a "substantive response off line from this meeting". He also promised to get back to leaders who has highlighted problems with connections out of Sheffield and asked for updates on the proposed re-opening of the Skipton-Colne line.