The Congress MP also accused the Trinamool Congress - which has held the railway ministry since 2009 - of "destroying" the railways.
"Cash-rich railways have been destroyed by Trinamool. I have no qualms in accepting that the condition of railways has deteriorated under Trinamool," said Choudhury.
Banerjee, who is currently the chief minister of West Bengal, held the railway portfolio from 2009 to May 2011.
Later on, her party's Dinesh Trivedi was given the portfolio as she moved to head the West Bengal government.
But Trivedi lost his job after he fell out with Banerjee over hiking the railway fare tariff against her wishes.
Roy, a trusted aide of Banerjee, took over as the railway minister in March this year.
In one of India's worst train tragedies, at least 35 passengers were killed, most of them were sleeping, and 25 injured when a coach of the Delhi-Chennai Tamil Nadu Express caught fire near Nellore in Andhra Pradesh early on Monday, officials said.