At a meeting of WYCA, the authority which oversees transport and infrastructure projects in West Yorkshire, it was claimed that train operators were running services with fewer carriages to ensure they would still run.
It follows problems throughout the summer after new timetables were introduced, with thousands of services in the north cancelled or severely delayed.
Members of WYCA, made up of council leaders from across the region, discussed a report into rail performance, which claimed some operators were seeing up to a quarter of their services arriving late to their destinations.
Leader of Leeds City Council Judith Blake, told the meeting: “There has been a huge furore since the timetables were introduced in May.
“We are here representing passengers and businesses that have suffered enormously from the effects on the north.
“There is still a significant way to go. The point I make regularly is that the chaos has resulted in too many trains being short-formed. Where you would expect three, four or more carriages, it has often been reduced to two, which has had a massive impact on passengers.
“There are seriously overcrowded stations where people cannot get on the trains, and once they get on they are often crammed like sardines on board.”
Bradford Council leader Susan Hinchcliffe said: “It’s so important that we get the high speed links through the region.
“But the performance of the current rail network is woeful.
“This, at a time when we are trying to grow our economy, is just sending us backwards.”
The report by WYCA claimed that, between April and September this year, only 73 per cent of TransPennine Express’s northern services and 87 percent of Northern’s train services had been arriving at their destinations on time.
Leader of the Leeds Liberal Democrats Coun Stewart Golton said: “(Late trains) have the biggest effect on peoples lives – they are being sanctioned for turning up late.
“That is the big question that needs to be answered. How are they going to get capacity onto tracks as soon as possible?”
Calderdale councillor Barry Collins (Lab) said: “I was one of the sardines travelling from Halifax to Leeds recently, dozens of people were stood back-to-back in the carriages.
“This is weeks and weeks and weeks after the timetable disaster.”
Members agreed to invite rail operators back to speak to the committee in February 2019.