Leeds City Council leader Judith Blake said it was "completely unacceptable" that the vast majority of disabled passengers didn't try to get on trains, particularly at peak times.
She spoke after it emerged that trains run by TransPennine Express in Leeds are squeezing in more passengers than the maximum capacity during peak hours, making it the operator's most crowded service in northern England.
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 Yorkshire Post understands that the stated capacity is already higher than the number of available seats, meaning in practice that there 40 per cent of passengers are standing.
Coun Blake told a meeting of the Rail North Committee, a subsidiary of Transport for the North, that official figures about the number of passengers being left at stations due to overcrowding were likely an underestimate, based on feedback from passengers.
She said: Coun Blake said: "We have to stress again and again what impact this is having on people with disabilities and I expect the vast majority don't even try to get on services, particularly at peak times, which is completely unacceptable.
"My real concern is the extent of over-crowding, particularly on TPE services. It is really frightening to see how many people are expected to get onto the trains. There is a six hour period of the travelling day which is experiencing severe overcrowding.
During the meeting, Greater Manchester metro mayor Andy Burnham highlighted the declining punctuality of trains run by TPE and Northern in recent weeks, adding: "There are a large number of unhappy passengers out there."
The meeting was told that rail operators had been focused on making sure this May saw a better performance than the previous May, when services were blighted by the timetable chaos, but later in the summer they faced a range of issues, including flooding and a lack of drivers, that "chipped away" at performance.
Leaders were told that passenger numbers were expected to increase by a third between June and September but that operators' plans were "slightly fragile" for the Autumn period, with an urgent need for more rolling stock as soon as possible.
Coun Blake said: "We remain very concerned about the Autumn and the fact that we will see higher passenger numbers and we need to be vigilant about the impact that is having on the travelling public."
The meeting was told that around £15m in funding had been left over from the previous control period, the five year time periods into which rail infrastructure funding is allocated.
At a previous meeting the board asked that the money be spent on making rail services in the North more resilient, including measures to stop train wheels locking in the autumn due to weather conditions and leaves.
But leaders were told today that it was unclear what had happened to this funding and whether the requested work had been done. Officials promised to contact Network Rail, the body responsible for rail infrastructure, for answers. Mr Burnham described the situation as "pathetic" and added "if it has not been spent it is a total disgrace".
Conservative Tees Valley mayor Ben Houchen said: "If we are expecting to take on more responsibility for the rail network in the North we need to get our house in order. We should already have that answer."