The Rail, Maritime and Transport (RMT) union, Aslef and the Transport Salaried Staffs Association (TSSA), said members' jobs and conditions, as well as the interests of passengers and taxpayers, were threatened by a lack of consultation.
The unions are seeking a judicial review after accusing the Coalition Government of rushing through the privatisation of the East Coast main line so it is completed before next year's General Election.
Union officials said ministers had "cut corners" and had not carried out a proper consultation with passenger groups and unions.
They are also challenging extensions to the Thameslink and Great Northern franchises.
Aslef general secretary Mick Whelan said: "It is imperative we raise the genuine concerns of all stakeholders but especially the employees, before this is rushed through. We cannot, in good conscience, allow the mistakes of the past to happen again."
RMT acting general secretary Mick Cash said: "After the scandal of this Government robbing the British taxpayer of a billion pounds in the scramble to privatise the Royal Mail it is shocking that they are engaging in the same tactics to try to hand the East Coast Mainline back to their friends in big business."
TSSA leader Manuel Cortes said: "The coalition knows only too well that rail franchising is not fit for purpose."