Passengers have been left aggrieved after the company's Leeds-to-Knottingley service was heavily scaled back, with several daily trains pulled from the timetable because of a driver shortage.
Only replacement bus services appear to be running from Pontefract Baghill.
Some passengers suggested this week that the Five Towns area has been singled out for particularly bad cuts, at the expense of other parts of the network.
Northern denies that is the case.
In a statement issued on Friday in response to the complaints, the company said: "Like any other business our colleagues can be affected by coronavirus, directly and indirectly, and this can impact the availability of our train crew on any given day.
"Whilst we do operate with additional staff it can sometimes be difficult to provide cover for every service.
"Therefore we have had to make the difficult decision to reduce service levels on some routes on our network.
"We have worked to minimise the impact of Covid and traincrew availability as much as possible but we are advising customers that there may be short notice alterations to services and they should check the details of their journey before they travel via http://nationalrail.co.uk/"We would like to apologise for any disruption that may occur as a result of the impact of coronavirus."
Local Democracy Reporting Service