Generally, train companies are looking for ways to recoup losses incurred by the desertion of passengers from train services following the disruption.
The cost-reduction programme will cut almost 100 out of 450 management jobs, according to the website FT.com.
Gerry Doherty, the officer responsible for National Express at the transport management union (TSSA), told the FT: "In the middle of this chaos they take out whole structures of management and then try to manage it almost at arm's length.
"I can't for the life of me see it's going to improve the lot for customers."
Consolidation
National Express, which operates nine out of 25 train franchises, plans to merge the head offices of its three London commuter services - WAGN Railway, Silverlink and c2c.
"We think larger and fewer franchises are better, but this must not mean letting swathes of management go with their expertise and knowledge," said Stewart Francis, chairman of the Rail Passengers' Council.
Because of the bank holiday on Monday, National Express was not available to comment on the concerns expressed by Mr Francis and the TSSA's Mr Doherty.
Previously, National Express said the consolidation of its facilities would not affect services. It also said the cost-cutting was not linked to the disruption caused by cracked rails.
Recouping losses
Railtrack, which operates the UK rail network, has struggled to meet deadlines to overhaul its infrastructure following the train crash at Hatfield last October.
Generally, train companies are looking for ways to recoup losses incurred by the desertion of passengers from train services following the disruption.
Virgin Trains, Great North Eastern Railway, and Midland Main Line have all announced price rises to take effect next month.
Additionally, a report from The Observer newspaper on Sunday said that Virgin is poised to sue Railtrack for inadequate compensation following the Hatfield crash.
The National Express Group, which began life as a UK coach company, serves more than 950 million passengers a year worldwide on its bus, train, tram, express coach and airport operations.