A letter from Rob McIntosh, a route managing director at Network Rail, to the Transport Secretary, describes the disruption that could be caused if the project is to be completed by 2024.
The document, which has emerged online, also says attempting to make further improvements "would add additional risk to the programme", although it is understood that parts of the line will be electrified, but not the entire route.
Mr Grayling has repeatedly highlighted the Government's £2.9bn investment in upgrades to the Victorian railway, which has long been blighted by delays and a lack of capacity, peaking this summer during the timetabling chaos.
Rail staff ‘fear for their safety’ as TransPennine Express passengers’ frustrations boil over, says Yorkshire MP Mr McIntosh said the work would eventually "transform" passengers' experience between York, Leeds and Manchester through "significantly" reduced journey times, more capacity on trains, and upgrades to stations along the route.
But he warned it "cannot be delivered without significant disruption" due to having to upgrade an old railway in the "inherently challenging" landscape of the Pennines.
Network Rail will carry out the works to minimise disruption around key seasonal economies such as tourism, university terms and Christmas markets, "but delivering this level of investment to ensure value is maximised cannot be done without disruption".
Trains will be diverted through other routes such as through the Calder Valley, but "in practice to achieve the improvements we are seeking we will need to close some part of this (trans-Pennine) route for up to 39 weeks per year between 2020 and 2024," Mr McIntosh said.
"This will see journey times increase by 15 to 25 minutes and also constrain capacity over the period."
Commenting on the letter, Mr McIntosh told The Yorkshire Post: "The message for me is that delivering £3bn of investment on one of the most contested parts of the network is going to be disruptive to local communities, economies and passengers.
"What we have put forward we think delivers the best benefits and outcomes for passengers in the shortest time scales while maintaining the connectivity of the community. "
Conservative MP for Thirsk and Malton Kevin Hollinrake said disruption was unfortunately inevitable with works "of that magnitude" while suggesting Ministers could ask Network Rail to potentially shorten the timescale.
The revelations also highlight the lack of other routes across the Pennines and the need to get on with building Northern Powerhouse Rail across the region by 2032, he said.
Mr Hollinrake added: "The Treasury and the Department for Transport (DfT) seem very supportive (of that idea), they are waiting for this business case from Transport for the North which we think will be with us by the end of the year, but I'm still hoping for a Budget commitment for that nevertheless to say 'all being well with the business case we're going to support it'."
The Department for Transport said the improvements were being phased over five years to "keep disruption to a minimum".
A spokeswoman said: “We are investing £13bn in transport in the north, and are planning to invest £3 billion upgrading the trans-Pennine route - one third of our budget for rail upgrades between 2019-24. This is our biggest planned investment project in the next five years, and will reduce journey times, increase capacity and improve stations.
“We are working closely with Network Rail and Transport for the North to deliver these vital improvements that passengers want and deserve as quickly as possible. However, we also want to keep disruption to a minimum, which is why the upgrade will be delivered in phases from Spring 2019.”
Meanwhile, Rail Minister Jo Johnson announced plans to make compensation for delays available to more Northern rail passengers.
The delay repay scheme currently only pays out for delays of 30 minutes or longer, but under the change passengers will be able to claim compensation for delays of 15 minutes.
The changes will mean that passengers delayed by between 15 and 29 minutes will be able to claim back compensation worth 25 per cent of the single fare.
Mr Johnson, who is attending the Transport for the North Board in Sheffield, said: "Passengers deserve a reliable train service, and when things do go wrong it is vital that they are compensated fairly."
The extension comes on top of the special compensation package announced for Northern and TransPennine Express passengers who experienced unacceptable disruption following the timetable changes earlier in the summer, the Department for Transport (DfT) said.
But that package is mainly focused on passengers in the north-west, despite many Yorkshire areas being affected.
Work is still being done by Northern rail, the DfT, along with Transport for the North and the Rail North Partnership to finalise commercial terms before the changes are introduced.
Northern's commercial director Mark Powles said: "We welcome the introduction of Delay Repay 15 later this year.
"We are putting in place the right measures to make it as easy as possible for our customers to claim compensation for delays to their services."
David Hoggarth, strategic rail director for Transport For The North, said: "This will be a welcome step forward for passengers who are inconvenienced by delays and is in addition to the previously announced special industry compensation package for those most disrupted by the May timetable changes.
"Our focus remains on ensuring the train operators and Network Rail continue to improve performance for passengers."
But Peter Vicary-Smith, chief executive of Which?, said: "While the introduction of Delay Repay 15 will provide some relief to passengers in the North who have suffered months of unacceptable delays, it fails to address the difficulties many passengers tell us they face in actually claiming compensation.
"Northern rail should now go further and make compensation automatic for all passengers so they aren't having to jump through hoops to get what they are owed."
Shadow Transport Secretary Andy McDonald called on the Government to stop a planned 3.2 per cent hike in fares and instead freeze prices along the route "as it is unacceptable that passengers should be even further out of pocket following months of disruption.”