Services on the troubled train operator TransPennine Express (TPE) may deteriorate further after it is nationalised, it is claimed.
It was announced
earlier this month that the government would run the service after customer complaints of poor service and cancelled trains.
A letter from the state-owned operator suggests some of the challenges may get worse in the weeks ahead.
However, the mayor of West Yorkshire called it a "fresh start".
TPE has been criticised for months over poor performance, with figures from the Office of Rail and Road showing that between January and March the operator cancelled 21.7% of the trains it runs across the North of England and into Scotland.
It will be run by the Operator of Last Resort (OLR) from Sunday.
It comes after the Labour mayors of West Yorkshire, South Yorkshire, Manchester, Liverpool and North of Tyne asked the government not to renew FirstGroup's contract to run the service when it expires on 28 May.
A letter - sent to local officials and seen by BBC Look North - said: "The change should be seamless for customers and all employees who wish to do so will transfer.
"Our immediate focus must be to re-establish relationships, re-engage colleagues and rebuild trust with passengers."
However, it also warned that it was clear from an initial review of TPE's current plans that "they were even more stretched than we had understood".
"A number of drivers have decided not to transfer, we start in half-term week including a bank holiday, which will reduce staff availability further, and there are several days of strikes to manage," the letter read.