In 2015, the Department for Transport said electrification of the whole link - which goes through Manchester, Leeds and York - would be complete by 2022.
Transport Secretary Chris Grayling has since said electrification will instead be used "where it makes a difference".
Shadow rail minister Rachael Maskell has called it "a slap in the face".
In an interview with the Daily Telegraph, Mr Grayling said: "We are not abandoning electrification, what we are doing is using electrification where it makes a difference.
"What we've got on the railways is technology we didn't have five or six years ago."
He said the use of bi-mode trains, which can travel on both electrified and non-electrified sections of a track, meant there were "places on the network you don't actually need to start digging everything up and putting in place overhead cables".
The project to electrify the route between Manchester and Leeds was announced in 2011 as part of the then chancellor George Osborne's ambition to create a northern economic "powerhouse".
The government said it would deliver more passenger capacity and shorten journey times.
However, the electrification was controversially paused in 2015 when a review into its costs and plans was carried out.
Speaking about this latest development, Ms Maskell said: "This is a slap in the face for the commuters and businesses in the North, including those in my constituency of York Central.
"Just six weeks ago the Tories promised the electrification of the TransPennine route as an integral part of the government's 'Northern Powerhouse'."
In an open letter to Mr Grayling, Greater Manchester mayor Andy Burnham said the north had "put up with second-class transport for too long".
He said the possible changes "would represent a major broken promise... and the derailment of the Northern Powerhouse".
Mr Grayling's announcement comes days after the government scrapped the planned electrification of three railway lines.
They included the routes between Cardiff and Swansea; between Windermere and Oxenholme in the Lake District; and between Kettering, Nottingham and Sheffield.
A Department for Transport spokesman said: "We are investing around Â£40 billion in our network as part of the biggest rail modernisation programme for over a century to provide faster journeys and more comfortable trains.
"This includes delivering improved journeys for passengers right across the North."

The DNC's computer network was infiltrated in a "serious" incident, said chairwoman Debbie Wasserman Schultz.
A cyber security firm has been hired to help, she said, to "kick out the intruders and secure our network".
Russia has denied any involvement in the hacking.
"I completely rule out a possibility that the [Russian] government or the government bodies have been involved in this," Dmitry Peskov, a Krelim spokesman, told Reuters in Moscow.
The hack was first reported by the Washington Post.
DNC officials said the hack did not expose personal or financial information but email and chat traffic had been stolen.
The group says the hackers, two separated "sophisticated adversaries", have now been expelled from the system, and the breach was first discovered in April.
"Both adversaries engage in extensive political and economic espionage for the benefit of the government of the Russian Federation and are believed to be closely linked to the Russian government's powerful and highly capable intelligence services," cyber security firm CrowdStrike said.
Other organisations targeted by the Russian groups include presidential nominees Hillary Clinton and Donald Trump's networks and some Republicans political action committees, according to the Washington Post.
Russian president Vladimir Putin has spoken highly about Mr Trump, who has suggested the US pull out of Nato and described Mr Putin as a man he admires.
"The security of our system is critical to our operation and to the confidence of the campaigns and state parties we work with," Mrs Wasserman Schultz said.
"When we discovered the intrusion, we treated this like the serious incident it is and reached out to [cyber security group] CrowdStrike immediately."
Hackers from Russia were also accused of hacking into President Obama's unclassified emails in 2015.
The railway route between Liverpool and Newcastle may not be fully electrified despite a promise by the previous government.
[NEXT_CONCEPT]
Russian government hackers breached Democratic National Committee computers to obtain opposition research on Republican Donald Trump, say officials.