Train manufacturer CAF recently made TPE aware of the problem with the brakes which means trains judder to a halt when they are stopping at slow speeds.
Thirsk and Malton MP Kevin Hollinrake said the delay was "disappointing" following the timetabling chaos which caused misery for passengers in the North this year.
TPE has asked the manufacturer to fix the issue so the new Nova 3 trains can begin operating on the route between Middlesbrough, Scarborough, York, Leeds, Huddersfield, Mancheter and Liverpool as soon as possible.
The operator is confident that customers will start to see new trains in service by Spring next year and the issue does not affect the other two new Nova fleets, Nova 2 and 1, which will be introduced next year.
All three fleets of new trains plus an extra 13m seats will be delivered by 2020, TPE said.
Tory MP Mr Hollinrake said: "Clearly it is important that the trains operate properly and are safe but any delays are disappointing after the difficult we have had this summer.
"People are bound to question TPE's competence here."
Tom Richmond: Government’s strategy for North has gone off the rails and the Budget proves itLeo Goodwin, TPE managing director, said: “While we are keen to start the roll out of the Nova 3s as soon as possible, it is important that we allow CAF to address the issue identified during the train testing process. It was hoped that our customers would start to experience these new trains before the end of the year, but we will all now have to wait until the New Year.
“This issue does not affect the other Nova fleets, we will start to see new trains in service by Spring next year, and we are still on track to complete the roll out of all three fleets of trains by 2020. This is a hugely exciting and ambitious project that will provide our customers with extra seats, extra space and a whole new experience when travelling with us.
“We will continue to work with CAF to ensure that we can get the trains onto our network as soon as possible. It may be a short delay to the programme, but it will definitely be worth the wait.”
This is why trains from Yorkshire to London will terminate in Peterborough in 2019 Richard Garner, UK director for CAF, said: “We are working closely with TPE to resolve the technical issue. Our trains undergo thorough, detailed testing in order to ensure that when they enter service, they provide the customer with a reliable, comfortable and high-quality service.
“When the Nova 3 trains enter service in the new year, we believe the customer will see a huge step change in their travelling experience.”
The announcement comes with Prime Minister Theresa May currently considering who to appoint as the new Rail Minister following the resignation of Jo Johnson over Brexit.