The situation faced by passengers using Northern rail services is totally unacceptable, Downing Street has said.
Transport Secretary Chris Grayling is expected to make a statement to MPs later as cancellations and delays continued despite the introduction of temporary timetables designed to halt the disruption.
READ MORE: Call for train users to be compensated after new interim timetable - removing 6% of services - is brought in
The Prime Minister's official spokesman said: "We have tremendous sympathy with everyone who has had their rail journey delayed or disrupted.
"What we have seen had been totally unacceptable."
Northern launched an eight-week interim timetable on Monday, removing 165 trains - 6% of services.
Areas affected include Manchester, Liverpool, Blackpool and the Lakes Line between Oxenholme and Windermere.
Govia Thameslink Railway (GTR) - which consists of Southern, Thameslink, Great Northern and Gatwick Express - is also running a temporary timetable enabling passengers to "arrange their journeys with greater confidence".
Some 230 daily services have been removed by GTR, which makes up 6% of scheduled trains.
Northern's policy is for passengers to only claim compensation based on the alternative timetable rather than previous versions.
The reduced timetables failed to stop Monday becoming the start of a third week of rail chaos with the number of trains either cancelled or more than 30 minutes late for Northern and GTR reaching 69 (7%) and 102 (8%) respectively by 12.30pm, according to the trains.im website.
The timing of all GTR and most Northern trains was changed on May 20 with the launch of new services and capacity.
Since then, hundreds of trains have been cancelled, with Mr Grayling blaming Government-owned Network Rail for delaying the approval of the new timetables amid late-running engineering projects.
Even before the new timetables, Northern services suffered frequent delays and cancellations.
New Network Rail punctuality data shows that between April 29 and May 26, more than one in three (35%) trains on the operator's Lancashire and Cumbria routes were delayed by at least five minutes.
This is the most since Arriva Rail North took over the franchise in April 2016.
The Mayor of Greater Manchester Andy Burnham said frustrated train commuters in the North should get substantial compensation and fare reductions, claiming Northern is in the "last chance saloon".
In a letter to the chairman of Transport for the North (TfN) John Cridland, the mayor said Northern is likely to benefit financially from the operation of the reduced timetable and if the company is not prepared to fund the compensation package and reduce fares voluntarily, then fines should be imposed to pay for it.
Mr Burnham also called for Northern passengers on affected routes to be allowed to use their tickets on other modes of transport such as TransPennine Express trains, buses and Metrolink.
He said: "Northern have already left people seriously out of pocket and turned their lives upside down with their chaotic services.
"I have heard countless stories of people forking out for taxis, hire cars, hotels and extra childcare - but unable to get compensation for it.
"Now that Northern are unilaterally cancelling thousands of services - that many season ticket holders have already paid for - passengers must be properly and fully compensated."
Northern insists it will still run more trains than it did before last month's timetable change, and expects to get back to a full timetable service by the end of July.
The firm's managing director David Brown has apologised for the "unacceptable service", and said they are working hard to fix the problems.
London Mayor Sadiq Khan said on Friday that disruption to GTR services is damaging the "international reputation" of the capital, and said the firm should be stripped of its franchise.
GTR said it is "very sorry for the significant disruption" and is "working with industry colleagues to introduce further changes that will progressively deliver improvement".
Mr Grayling has said he is in regular discussions with train operators, adding that the new timetable will ultimately deliver hundreds more services.