New figures released by rail bosses show that during peak hours of 7am to 10am and 4pm to 7pm, the operator's trains are squeezing in nearly three per cent more passengers on average than the stated capacity.
The rate of overcrowding is much higher in Leeds than any other major city in the North. In Manchester trains are operating at eight per cent under capacity at peak times, while in Sheffield peak time trains are running at 34 per cent under capacity.
The strategic body, whose subsidiary Rail North is responsible for managing Northern and TPE, says passenger crowding is a significant concern and that "both operators are in the process of bringing in new trains, in part to address the capacity problems".
The report, which will be discussed by the North's political leaders on Wednesday, says the performance of both operators are still below the targets set out when they were awarded the franchises, despite improving since last year's rail chaos in the North.
In late May and June 83.3 per cent of TPE trains were on time, up from 75.5 per cent at the same time last year but still target and a worse performance than the rest of the year. Northern's rate of 84.7 per cent was also higher than for last May.
A spokesperson for TransPennine Express said: “We know that our services across the Pennines can be very busy, especially at peak times, following a double in the number of customers travelling over the past decade.
"That’s why we are delivering an investment of £500 million on our new Nova trains, which offer many more seats compared to our existing trains, and will start running across our network in the next few weeks and months, with Leeds one of the cities that will first benefit.”
A spokesman for Northern said: “Rail usage has significantly increased in recent years, particularly in and around the main towns and cities in the north of England.
“Northern is investing in major improvements to help customers and, earlier this month, introduced the first of our brand new trains running to and from Leeds. More will follow throughout this year as the £500m investment in new trains not only increases capacity, but also gives our customers a step-change in journey experience, with free WiFi, air conditioning and at-seat charging points."
The disruption caused by the botched introduction of a new timetable by Northern last summer cost the economy millions and helped to prompt the Williams review, a root and branch review of Britain's railways led by former British Airways chief executive Keith Williams.
And earlier this month the Blake Jones Review, also set up in the aftermath of the timetable chaos, made nine recommendations to improve services, including more local decision-making and more effective communication between rail operators and passengers.
The report said the North’s rail infrastructure suffers from “overcrowding, short formed trains, reliability issues and bottlenecks”.
The report's author, Leeds city council leader Judith Blake, who leads on transport for the West Yorkshire Combined Authority, said: “One of the key promises in the franchise commitments was to reduce overcrowding at peak times and this simply is not happening.
“With the autumn peak approaching we urgently require operators to demonstrate they have sufficient rolling stock in place to ensure passengers are not left on platforms.
“The North will only have the modern reliable rail network it needs with investment in extra capacity. In the short and medium terms this means investment in more and longer trains and associated rail infrastructure improvements, and in the long term includes HS2 and Northern Powerhouse Rail with a line through Bradford City Centre.”