In a message seen by The Yorkshire Post, Transport for the North chief executive Tim Wood said leaked plans for the flagship project to follow the line of the existing Transpennine Route via Huddersfield would "significantly undermine" its vision for rail links across the North.
The Yorkshire Post reported on Monday that the Department for Transport had drawn up plans for much greater investment in the Transpennine Route Upgrade (TRU) between Leeds and Manchester in a move that would cut journey times and improve reliability.
Officials say the investment of up to £11.5bn would cut the number of minutes lost to delays in half and create 15 new opportunities for freight per day.
But northern leaders fear that by developing Northern Powerhouse Rail along the route of TRU and not building a new line, it would mean Bradford would miss out on a high speed rail connection thought to be vital for the city's economic fortunes.
Amid fears of tensions between Boris Johnson and Chancellor Rishi Sunak over the cost of Tory manifesto promises, the Prime Minister's spokesman yesterday said the Government was "absolutely" going ahead with plans for a new line between Leeds and Manchester.
But Mr Wood's note to TfN members said Grant Shapps' Department for Transport was looking for funding for an option "which if Ministers should wish, could facilitate NPR to be routed via Huddersfield".
He said: "Previously referred to as a ‘TRU Plus’ option this could significantly undermine the TfN Board’s preferred route choice for NPR between Manchester and Leeds (new line via Central Bradford)."
He said this was "not acceptable from an NPR perspective" but welcomed the plans for extra track and full electrification which would improve capacity and performance on the busy Transpennine route.
Mr Wood said he had been told by DfT officials that £1.5bn set to be invested in TRU included £45m to keep open the possibility of the so-called 'option G' of developing NPR along the same route.
He said he'd been told there are two central options being considered between Manchester and Leeds, one via Huddersfield plus a connection between Marsden in West Yorkshire and Manchester and TfN's preferred new line route via central Bradford.
Government sources insist no decision has yet been taken and that they will all be subject to the Integrated Rail Plan, which will set out how NPR, HS2 and TRU will fit together and is due to be published later this year.
A Government spokeswoman said: “The Integrated Rail Plan will soon outline exactly how major rail projects, including HS2 phase 2b, the Transpennine Route Upgrade and other transformational projects such as Northern Powerhouse Rail, will work together to deliver the reliable train services that passengers across the North and Midlands need and deserve.”
On Monday West Yorkshire metro mayor Tracy Brabin spoke to Mr Shapps and said the Transport Secretary "refuted recent reports about the Government scaling back NPR in Bradford".
She added: "He reaffirmed his commitment to the city, acknowledging the need for Bradford’s young people in particular to be better connected to infrastructure and greater opportunities."
It comes amid reports that the Prime Minister and Chancellor are split over the NPR project, which Boris Johnson promised to fund in a speech in July 2019.
According to the HuffPost UK website the Treasury is attempting to delay the publication of the Integrated Rail Plan to coincide with Richmond MP Mr Sunak’s spending review in autumn, while No 10 wants it made public as soon as possible.