The Transport for the North performance report for Northern and TransPennine Express said levels of reliability are now lower than in the same period for 2018, when the North was still recovering from the timetable chaos of May.
Rail officials say the operators have been hit particularly hard by severe weather events such as the flood risk in the Derbyshire town of Whaley Bridge, cancellations caused by a lack of a train crew and train failures.
But Tom Davidson, Transport Planner at Transport for the North, wrote: "The downturn in reliability is a significant concern going into the Autumn, when demand traditionally increases and the effects of leaf fall can have an impact on performance".
As concerns mounted over the months ahead for rail services in the North, train passengers on a key commuter route in Yorkshire called for answers after being forced to pack into carriages "like sardines", with questions raised over health and safety.
The York-Harrogate-Leeds line, which is operated by Northern, has seen vast improvements in recent months, with additional services launched, along with a new fleet of modern trains.
However, commuters say the service has gone "back to the bad old days" over the past few weeks, with the reintroduction of older trains, just two carriages at peak journey times and regular delays.
A root and branch review of Britain's railways, independently chaired by former British Airways executive Keith Williams, is expected to report back later this year.
In July a review by Leeds City Council leader Judith Blake and then-Rail Minister Andrew Jones recommended a new "Passenger Promise" putting customers "at the centre of decision-making across the industry" and greater accountability.
Coun Blake, a member of the TfN board, said and West Yorkshire Combined Authority's transport lead, said: "“It’s extremely disappointing to get the confirmation that passengers in the North continue to experience unacceptable performance in terms of punctuality and reliability.
"Sadly this is nothing new but the travelling public of the North deserve much better. In the short term we will continue to put the train operators under close scrutiny to improve performance.
"In the longer term we are clear our region will only have the modern reliable rail network it needs with investment in extra capacity, including HS2 and Northern Powerhouse Rail with a line through Bradford city centre, and we are making that case to Government strongly with partners across the North through the Connecting Britain campaign.”
The report for the Rail North Partnership, a subsidiary of TfN responsible for managing Northern and TransPennine, will be discussed at a meeting tomorrow in Manchester.
Mr Davidson wrote that following a period of recovery from December 2018 onwards, "performance has continued to deteriorate for both operators".
He added: "Passenger crowding continues to be significant concern for both operators, particularly ahead of the increase in peak demand typically seen in September / October 2019."
For TransPennine Express, its public performance measure - equating to the number of trains running on time - was 70.9 per cent between July 21 and August 17, compared with 75.7 per cent for the same period last year and 85.2 per cent in the period between December 9.
Over the 28 days, an average of 42 trains were cancelled or part-cancelled every day, representing 12.9 per cent of all services. The operator says 60 per cent of the cancellations were caused by other operators or Network Rail.
Northern's public performance measure was 79.4 per cent, down from 82.2 per cent a year ago and 86.8 per cent between December and May.
An average of 139 trains a day were cancelled or part-cancelled each day, representing 5.3 per cent of services. Of these, 90 each day were caused by Northern itself.
At the height of the timetable chaos in late May and early June last year, Northern's public performance measure was 70 per cent and TransPennine's was 63 per cent.
A spokesperson for TransPennine Express said: “Last month our customers experienced some disruption to their journeys. This was due to a number of factors, the most significant being weather events such as flooding and extreme heat.
"Performance has improved this month and we are working hard to ensure that we continue to provide the best possible service for our customers.”
A spokesman for Northern said: “Our performance has been steadily improving over the past 12 months as we have worked hard to bring stability and reliability to our services.
“We know there is more to do, and our customers were impacted over the summer by extreme weather causing flooding and damage to overhead lines and disruption to many rail services across the country
“Northern is delivering the biggest transformation of local rail for a generation, with 18 of our 101 new trains already in service and driver training on a further 20 trains taking place right now.”