Officials at Transport for the North are working on six options for the route connecting the two biggest cities in northern England as part of the £39bn Northern Powerhouse Rail project and were aiming to narrow them down to one by the beginning of next year.
But after Mr Johnson said in a speech in Manchester this weekend that he had "tasked officials to accelerate their work on these plans so that we are ready to do a deal in the autumn", the deadline may need to move forward.
TfN's chairman John Cridland told a meeting of the strategic transport authority's board in Leeds, said: "We may need to speed that work up in order to be ready to get the investment capital if there is immediate follow-up from this announcement."
Northern political leaders have warned that a commitment was needed for the entire Northern Powerhouse Rail network connecting Liverpool and Hull with Newcastle, Sheffield, Manchester and Leeds.
Mr Cridland, a former Director-General of the Confederation of British Industry, said it was vital for TfN to push for the 'full monty' ambition of coast-to-coast coverage. He added: "If there is an opportunity like this, we do need to look at what we are doing to seize the opportunity while the political window is open."
TfN chief executive Barry White told northern leaders that he met with Mr Johnson in Manchester and was asked what needed to be done for a deal to be completed by autumn. He suggested that rather than a Hybrid Bill process like that used for HS2 a quicker development consent order could be used.
Labour politicians at the board meeting said Mr Johnson's pledge needed to just the start of investment in the North.
Liverpool metro mayor Steve Rotheram said he was "disappointed" by the announcement, adding: "I believe tactically this was picking us off, we need to be very careful it doesn't become piecemeal.
"The whole idea and ethos of us working together is because we believe that connectivity between East and West is the important goal. Just promising small pieces of it doesn't do what we set out strategically to do as a board."
Darren Hale, deputy leader of Hull council, said: "As we are out one coastal fringe I completely concur, we wouldn't want this to become a replacement for NPR, it could be the potential for an early win and then it stops there.
"But any investment in rail in the North, if it comes to fruition, can only be a good thing as long as that is the start of the journey not the end."
Greater Manchester metro mayor Andy Burnham said: "It is a change of tone and emphasis that we have not had in the last couple of years. That is a positive thing. When there is a renewed sense of focus on the North, this is not a time to lower our ambitions for the North of England, it is time to do the opposite.
"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.
"We must not lower our ambitions, both in the geographical spread of what we are asking for and the quality of what we are asking for at the heart of our cities."
But Tory Ben Houchen, mayor of the Tees Valley, said: "Having spoken to the Prime Minister about his ambitions for Northern Powerhouse Rail, the plans are much more expansive than just Manchester to Leeds.
"I think the reason for the early announcement, and this should be put on record, is the hard work even in the first few days that [Richmond MP and new Chief Secretary to the Treasury] Rishi Sunak has had on trying to drive this forward.
"He has been huge supporter of Transport for the North trying to upgrade rail travel and the influence he has had on the PM in the first few days to make that announcement.
"This is not something that can be looked at in isolation, the Manchester to Leeds part of NPR was the most difficult and complex to achieve, the easiest part will be the East Coast.
"Signalling that they want to tackle the most complex bit would suggest there is plenty to go at and the rest of it needs to happen but the signals are there that it isn't just Manchester down to Leeds, there is a will and a want to complete Northern Powerhouse Rail."