The deal follows a recent government pledge to renationalise nearly all passenger rail services within five years.
Mick Lynch, general secretary of the Rail, Maritime and Transport (RMT) union said the move “risks further short-changing passengers and undermining the financial sustainability of the capital’s transport system”.
“It is deeply concerning that while other parts of our rail network are being brought back into public hands, the Elizabeth Line is being left to funnel profits to private operators.”